<HTML><HEAD><TITLE>headreco report</TITLE></HEAD><BODY><pre>2021-05-11 21:09:03 [DEBUG] C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\cli\headreco.py all MCI_PAPER mci_paper.nii
2021-05-11 21:09:03 [INFO ] ========================================================================
2021-05-11 21:09:03 [INFO ] PREPARING VOLUMES FOR MESHING
2021-05-11 21:09:03 [INFO ] ========================================================================
2021-05-11 21:09:03 [INFO ] Copying input files to m2m_MCI_PAPER
2021-05-11 21:09:05 [INFO ] Copying T1fs.nii.gz to T1fs_conform.nii.gz
2021-05-11 21:09:07 [INFO ] Preparing to segment
2021-05-11 21:09:07 [INFO ] Starting MATLAB
2021-05-11 21:09:07 [INFO ] ========================================================================
2021-05-11 21:09:07 [DEBUG] Running matlab -nosplash -nodesktop -wait -logfile "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\spmcat.log" -r "addpath('C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\msh','C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\resources\spm12');try,segment_SPM('C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\resources\templates','C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\spm\T1fs_conform.nii',[],0.01,3); segment_CAT('C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\T1fs_conform.nii','C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\resources\templates',1);catch ME,rethrow(ME);end,exit;"
2021-05-11 22:56:53 [INFO ] Binarizing tissue probability maps
2021-05-11 22:57:03 [INFO ] Creating unity.xfm and ref_FS.nii.gz
2021-05-11 22:57:04 [INFO ] Moving forward deformation field
2021-05-11 22:57:04 [INFO ] Moving affine MNI to subject space transformations
2021-05-11 22:57:04 [INFO ] Copying T1 image
2021-05-11 22:57:04 [INFO ] Copying bias corrected T1 image
2021-05-11 22:57:06 [INFO ] Moving and compressing warped priors and templates
2021-05-11 22:57:12 [INFO ] ========================================================================
2021-05-11 22:57:12 [INFO ] Preparation time: 01:48:09
2021-05-11 22:57:12 [INFO ] ========================================================================
2021-05-11 22:57:12 [INFO ] PREPARING SURFACES FROM CAT12
2021-05-11 22:57:12 [INFO ] ========================================================================
2021-05-11 22:57:12 [INFO ] Loading files...
2021-05-11 22:57:12 [INFO ] Expanding left hemisphere
2021-05-11 22:57:12 [DEBUG] Expanding
2021-05-11 23:00:20 [DEBUG] Cleaning
2021-05-11 23:00:20 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off"
2021-05-11 23:04:41 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:04:41 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off
2021-05-11 23:04:41 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:04:41 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off'
2021-05-11 23:04:41 [DEBUG] Resampling to a vertex density of 0.5
2021-05-11 23:04:41 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off"
2021-05-11 23:06:36 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:06:36 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off
2021-05-11 23:06:36 [DEBUG] Uniform remeshing ...
2021-05-11 23:06:36 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:06:36 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off'
2021-05-11 23:06:36 [DEBUG] Cleaning
2021-05-11 23:06:36 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off"
2021-05-11 23:06:49 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:06:49 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off
2021-05-11 23:06:49 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:06:49 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off'
2021-05-11 23:06:50 [DEBUG] Uniform remeshing
2021-05-11 23:06:50 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off"
2021-05-11 23:07:26 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:07:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off
2021-05-11 23:07:26 [DEBUG] Uniform remeshing ...
2021-05-11 23:07:26 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:07:26 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off'
2021-05-11 23:07:26 [DEBUG] Cleaning
2021-05-11 23:07:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off"
2021-05-11 23:07:39 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:07:39 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off
2021-05-11 23:07:39 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:07:39 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off'
2021-05-11 23:07:39 [INFO ] Expanding right hemisphere
2021-05-11 23:07:40 [DEBUG] Expanding
2021-05-11 23:10:56 [DEBUG] Cleaning
2021-05-11 23:10:56 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off"
2021-05-11 23:14:33 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:14:33 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off
2021-05-11 23:14:33 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:14:33 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off'
2021-05-11 23:14:33 [DEBUG] Resampling to a vertex density of 0.5
2021-05-11 23:14:33 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off"
2021-05-11 23:16:02 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:16:02 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off
2021-05-11 23:16:02 [DEBUG] Uniform remeshing ...
2021-05-11 23:16:02 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:16:02 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off'
2021-05-11 23:16:02 [DEBUG] Cleaning
2021-05-11 23:16:02 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off"
2021-05-11 23:16:15 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:16:15 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off
2021-05-11 23:16:15 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:16:15 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off'
2021-05-11 23:16:15 [DEBUG] Uniform remeshing
2021-05-11 23:16:15 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off"
2021-05-11 23:16:34 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:16:34 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off
2021-05-11 23:16:34 [DEBUG] Uniform remeshing ...
2021-05-11 23:16:34 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:16:34 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off'
2021-05-11 23:16:34 [DEBUG] Cleaning
2021-05-11 23:16:34 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off"
2021-05-11 23:16:48 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:16:48 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off
2021-05-11 23:16:48 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:16:48 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off'
2021-05-11 23:16:48 [INFO ] Voxelizing left hemisphere
2021-05-11 23:16:48 [DEBUG] Creating left.nii.gz from left.off
2021-05-11 23:16:50 [DEBUG] Making splits in z direction, tracing in x
2021-05-11 23:18:43 [INFO ] Voxelizing right hemisphere
2021-05-11 23:18:43 [DEBUG] Creating right.nii.gz from right.off
2021-05-11 23:18:45 [DEBUG] Making splits in z direction, tracing in x
2021-05-11 23:20:44 [INFO ] Preparing to join hemispheres and extract ventricles
2021-05-11 23:20:45 [INFO ] Joining CAT and SPM white matter segmentations
2021-05-11 23:20:52 [INFO ] Preparing mask for joining hemispheres
2021-05-11 23:21:06 [INFO ] Preparing ventricles
2021-05-11 23:21:15 [DEBUG] Generating surface mesh from join_all.nii.gz
2021-05-11 23:21:15 [DEBUG] Eroding
2021-05-11 23:21:16 [DEBUG] Creating initial mesh
2021-05-11 23:21:18 [DEBUG] Keeping maximum 1 largest shell(s) with minimum area of 1
2021-05-11 23:21:18 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all_ERO_mesh.off" -a 2.0 --no-clean -q --shells 1 --splitShells --shellMinArea 1 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii"
2021-05-11 23:21:23 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:21:23 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all_ERO_mesh.off
2021-05-11 23:21:23 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:21:23 [DEBUG] Processing join_all.nii1.off
2021-05-11 23:21:23 [DEBUG] Cleaning
2021-05-11 23:21:23 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off"
2021-05-11 23:21:33 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:21:33 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:21:33 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:21:33 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off'
2021-05-11 23:21:33 [DEBUG] Expanding
2021-05-11 23:21:37 [DEBUG] Moved 26506 of 26508 vertices
2021-05-11 23:21:41 [DEBUG] Moved 26503 of 26508 vertices
2021-05-11 23:21:44 [DEBUG] Moved 26488 of 26508 vertices
2021-05-11 23:21:47 [DEBUG] Moved 26471 of 26508 vertices
2021-05-11 23:21:51 [DEBUG] Moved 26409 of 26508 vertices
2021-05-11 23:21:55 [DEBUG] Moved 26107 of 26508 vertices
2021-05-11 23:21:55 [DEBUG] Cleaning
2021-05-11 23:21:55 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off"
2021-05-11 23:22:26 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:22:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:22:26 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:22:26 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off'
2021-05-11 23:22:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.stl"
2021-05-11 23:22:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:22:26 [DEBUG] Loading ..98%
2021-05-11 23:22:26 [DEBUG] INFO- Loaded 23330 vertices and 46660 faces.
2021-05-11 23:22:33 [DEBUG] 0% done
2021-05-11 23:22:33 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.stl'
2021-05-11 23:22:33 [DEBUG] Resampling to a vertex density of 0.5
2021-05-11 23:22:33 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off"
2021-05-11 23:22:44 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:22:44 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:22:44 [DEBUG] Uniform remeshing ...
2021-05-11 23:22:44 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:22:44 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off'
2021-05-11 23:22:44 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1_resampled.stl"
2021-05-11 23:22:44 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:22:45 [DEBUG] Loading ..98%
2021-05-11 23:22:45 [DEBUG] INFO- Loaded 21798 vertices and 43596 faces.
2021-05-11 23:22:51 [DEBUG] 0% done
2021-05-11 23:22:51 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1_resampled.stl'
2021-05-11 23:22:51 [DEBUG] Cleaning
2021-05-11 23:22:51 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off"
2021-05-11 23:22:56 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:22:56 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:22:56 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:22:56 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off'
2021-05-11 23:22:56 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1_resampled_clean.stl"
2021-05-11 23:22:56 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:22:56 [DEBUG] Loading ..98%
2021-05-11 23:22:56 [DEBUG] INFO- Loaded 21798 vertices and 43596 faces.
2021-05-11 23:23:03 [DEBUG] 0% done
2021-05-11 23:23:03 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1_resampled_clean.stl'
2021-05-11 23:23:03 [DEBUG] Smoothing 5 time(s)
2021-05-11 23:23:03 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off"
2021-05-11 23:23:03 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:23:03 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:23:04 [DEBUG] Loading ..98%
2021-05-11 23:23:04 [DEBUG] INFO- Loaded 21798 vertices and 43596 faces.
2021-05-11 23:23:04 [DEBUG] 0% done
2021-05-11 23:23:04 [DEBUG] Smoothing 5 steps.
2021-05-11 23:23:04 [DEBUG] INFO- Lambda: 0.500000
2021-05-11 23:23:10 [DEBUG] 99 % done - 1 steps left
2021-05-11 23:23:10 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off'
2021-05-11 23:23:10 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1_resampled_clean_smoothed.stl"
2021-05-11 23:23:10 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:23:11 [DEBUG] Loading ..98%
2021-05-11 23:23:11 [DEBUG] INFO- Loaded 21798 vertices and 43596 faces.
2021-05-11 23:23:17 [DEBUG] 0% done
2021-05-11 23:23:17 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1_resampled_clean_smoothed.stl'
2021-05-11 23:23:17 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-11 23:23:17 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:23:17 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:23:17 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-11 23:23:17 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:23:18 [DEBUG] Loading ..98%
2021-05-11 23:23:18 [DEBUG] INFO- Loaded 21798 vertices and 43596 faces.
2021-05-11 23:23:19 [DEBUG] 0% done
2021-05-11 23:23:19 [DEBUG] Removing Spikes.
2021-05-11 23:23:19 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:23:19 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-11 23:23:19 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:23:19 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:23:19 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:23:20 [DEBUG] INFO- 26 intersecting triangles have been selected (in selection).
2021-05-11 23:23:21 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:23:23 [DEBUG] INFO- No intersecting triangles detected.
2021-05-11 23:23:23 [DEBUG] INFO- *** Cleaning iteration 1 ***
2021-05-11 23:23:23 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:23:23 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:23:23 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:23:25 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:23:25 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.422734 (24.220873 DEGs)
2021-05-11 23:23:25 [DEBUG] INFO- *** Triangulation Report ***
2021-05-11 23:23:25 [DEBUG] INFO- V: 21745
2021-05-11 23:23:25 [DEBUG] INFO- E: 65235
2021-05-11 23:23:25 [DEBUG] INFO- T: 43490
2021-05-11 23:23:25 [DEBUG] INFO- Boundary: 0 components.
2021-05-11 23:23:25 [DEBUG] INFO- Handles: 1.
2021-05-11 23:23:25 [DEBUG] INFO- Shells: 1.
2021-05-11 23:23:25 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-11 23:23:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1_resampled_clean_smoothed_spike.stl"
2021-05-11 23:23:25 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:23:26 [DEBUG] Loading ..98%
2021-05-11 23:23:26 [DEBUG] INFO- Loaded 21798 vertices and 43596 faces.
2021-05-11 23:23:32 [DEBUG] 0% done
2021-05-11 23:23:32 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1_resampled_clean_smoothed_spike.stl'
2021-05-11 23:23:32 [DEBUG] Uniform remeshing
2021-05-11 23:23:32 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off"
2021-05-11 23:23:42 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:23:42 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:23:42 [DEBUG] Uniform remeshing ...
2021-05-11 23:23:42 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:23:42 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off'
2021-05-11 23:23:42 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1_resampled_clean_smoothed_spike_remesh.stl"
2021-05-11 23:23:42 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:23:43 [DEBUG] Loading ..97%
2021-05-11 23:23:43 [DEBUG] INFO- Loaded 21451 vertices and 42902 faces.
2021-05-11 23:23:49 [DEBUG] 0% done
2021-05-11 23:23:49 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1_resampled_clean_smoothed_spike_remesh.stl'
2021-05-11 23:23:49 [DEBUG] Cleaning
2021-05-11 23:23:49 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off"
2021-05-11 23:23:53 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:23:53 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off
2021-05-11 23:23:53 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:23:53 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off'
2021-05-11 23:23:53 [INFO ] Joining hemispheres
2021-05-11 23:23:53 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off" -a 2.0 --shells 2 -j -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off"
2021-05-11 23:23:53 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:23:53 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\left.off
2021-05-11 23:23:55 [DEBUG] Loading ..99%
2021-05-11 23:23:55 [DEBUG] INFO- Loaded 58810 vertices and 117616 faces.
2021-05-11 23:23:56 [DEBUG] Loading ..97%
2021-05-11 23:23:56 [DEBUG] INFO- Loaded 21451 vertices and 42902 faces.
2021-05-11 23:23:56 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\join_all.nii1.off was joined.
2021-05-11 23:23:56 [DEBUG] 0% done
2021-05-11 23:24:05 [DEBUG] INFO- 1331 intersecting triangles have been selected.
2021-05-11 23:24:06 [DEBUG] INFO- Number of triangles inside: 4123
2021-05-11 23:24:15 [DEBUG] INFO- 1331 intersecting triangles have been selected.
2021-05-11 23:24:16 [DEBUG] INFO- Number of triangles inside: 8350
2021-05-11 23:24:16 [DEBUG] INFO- first 0; second 0
2021-05-11 23:24:17 [DEBUG] INFO- Removed the smallest 7 of 9 shells
2021-05-11 23:24:17 [DEBUG] INFO- USING joinBoundaryLoops2
2021-05-11 23:24:17 [DEBUG] 0% done
2021-05-11 23:24:21 [DEBUG] 0% done
2021-05-11 23:24:21 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:24:21 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-11 23:24:21 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:24:21 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:24:21 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:24:27 [DEBUG] INFO- 5 intersecting triangles have been selected (in selection).
2021-05-11 23:24:31 [DEBUG] INFO- 14 intersecting triangles have been selected (in selection).
2021-05-11 23:24:35 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:24:47 [DEBUG] INFO- No intersecting triangles detected.
2021-05-11 23:24:47 [DEBUG] INFO- *** Cleaning iteration 1 ***
2021-05-11 23:24:47 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:24:47 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:24:47 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:24:53 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:24:57 [DEBUG] 100% done
2021-05-11 23:24:57 [DEBUG] INFO- *** Cleaning iteration 2 ***
2021-05-11 23:24:57 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:24:57 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:24:57 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:25:03 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:25:07 [DEBUG] 100% done
2021-05-11 23:25:07 [DEBUG] INFO- *** Cleaning iteration 3 ***
2021-05-11 23:25:07 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:25:07 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:25:07 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:25:13 [DEBUG] INFO- 3 intersecting triangles have been selected (in selection).
2021-05-11 23:25:17 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:25:29 [DEBUG] INFO- No intersecting triangles detected.
2021-05-11 23:25:29 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.269019 (15.413659 DEGs)
2021-05-11 23:25:29 [DEBUG] INFO- *** Triangulation Report ***
2021-05-11 23:25:29 [DEBUG] INFO- V: 74149
2021-05-11 23:25:29 [DEBUG] INFO- E: 222447
2021-05-11 23:25:29 [DEBUG] INFO- T: 148298
2021-05-11 23:25:29 [DEBUG] INFO- Boundary: 0 components.
2021-05-11 23:25:29 [DEBUG] INFO- Handles: 1.
2021-05-11 23:25:29 [DEBUG] INFO- Shells: 1.
2021-05-11 23:25:29 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off'
2021-05-11 23:25:29 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off" -a 2.0 --shells 2 -j -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off"
2021-05-11 23:25:29 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:25:29 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off
2021-05-11 23:25:31 [DEBUG] Loading ..99%
2021-05-11 23:25:31 [DEBUG] INFO- Loaded 74149 vertices and 148298 faces.
2021-05-11 23:25:33 [DEBUG] Loading ..99%
2021-05-11 23:25:33 [DEBUG] INFO- Loaded 58159 vertices and 116314 faces.
2021-05-11 23:25:33 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\segment\cat\surf\right.off was joined.
2021-05-11 23:25:34 [DEBUG] 0% done
2021-05-11 23:25:51 [DEBUG] INFO- 1398 intersecting triangles have been selected.
2021-05-11 23:25:54 [DEBUG] INFO- Number of triangles inside: 8342
2021-05-11 23:26:10 [DEBUG] INFO- 1398 intersecting triangles have been selected.
2021-05-11 23:26:13 [DEBUG] INFO- Number of triangles inside: 4326
2021-05-11 23:26:13 [DEBUG] INFO- first 0; second 0
2021-05-11 23:26:14 [DEBUG] INFO- Removed the smallest 4 of 6 shells
2021-05-11 23:26:14 [DEBUG] INFO- USING joinBoundaryLoops2
2021-05-11 23:26:14 [DEBUG] 0% done
2021-05-11 23:26:17 [DEBUG] 0% done
2021-05-11 23:26:17 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:26:17 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-11 23:26:17 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:26:36 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:26:36 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:26:55 [DEBUG] INFO- 20 intersecting triangles have been selected (in selection).
2021-05-11 23:27:01 [DEBUG] INFO- 17 intersecting triangles have been selected (in selection).
2021-05-11 23:27:07 [DEBUG] INFO- Removed the smallest 1 of 2 shells
2021-05-11 23:27:09 [DEBUG] INFO- 21 intersecting triangles have been selected (in selection).
2021-05-11 23:27:14 [DEBUG] INFO- Removed the smallest 1 of 2 shells
2021-05-11 23:27:15 [DEBUG] INFO- 9 intersecting triangles have been selected (in selection).
2021-05-11 23:27:22 [DEBUG] INFO- 13 intersecting triangles have been selected (in selection).
2021-05-11 23:27:29 [DEBUG] INFO- 8 intersecting triangles have been selected (in selection).
2021-05-11 23:27:29 [DEBUG] INFO- Stage: Laplacian Smooth (1)
2021-05-11 23:27:49 [DEBUG] INFO- 8 intersecting triangles have been selected.
2021-05-11 23:27:49 [DEBUG] INFO- Laplacian smoothing of selected triangles.
2021-05-11 23:27:49 [DEBUG] INFO- Stage: Remove and Fill (7)
2021-05-11 23:27:49 [DEBUG] INFO- 3 intersecting triangles have been selected (in selection).
2021-05-11 23:27:59 [DEBUG] INFO- Removed the smallest 1 of 2 shells
2021-05-11 23:27:59 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:28:18 [DEBUG] INFO- No intersecting triangles detected.
2021-05-11 23:28:18 [DEBUG] INFO- *** Cleaning iteration 1 ***
2021-05-11 23:28:18 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:28:39 [DEBUG] INFO- Removed the smallest 1 of 2 shells
2021-05-11 23:28:39 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:28:39 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:28:53 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:29:00 [DEBUG] 100% done
2021-05-11 23:29:00 [DEBUG] INFO- *** Cleaning iteration 2 ***
2021-05-11 23:29:00 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:29:00 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:29:00 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:29:14 [DEBUG] INFO- 5 intersecting triangles have been selected (in selection).
2021-05-11 23:29:20 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:29:44 [DEBUG] INFO- No intersecting triangles detected.
2021-05-11 23:29:44 [DEBUG] INFO- *** Cleaning iteration 3 ***
2021-05-11 23:29:44 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:29:44 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:29:44 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:29:58 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:30:05 [DEBUG] 100% done
2021-05-11 23:30:05 [DEBUG] INFO- *** Cleaning iteration 4 ***
2021-05-11 23:30:05 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:30:05 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:30:05 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:30:27 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:30:27 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.269019 (15.413659 DEGs)
2021-05-11 23:30:27 [DEBUG] INFO- *** Triangulation Report ***
2021-05-11 23:30:27 [DEBUG] INFO- V: 126108
2021-05-11 23:30:27 [DEBUG] INFO- E: 378324
2021-05-11 23:30:27 [DEBUG] INFO- T: 252216
2021-05-11 23:30:27 [DEBUG] INFO- Boundary: 0 components.
2021-05-11 23:30:27 [DEBUG] INFO- Handles: 1.
2021-05-11 23:30:27 [DEBUG] INFO- Shells: 1.
2021-05-11 23:30:27 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off'
2021-05-11 23:30:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" -a 2.0 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off"
2021-05-11 23:30:28 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:30:28 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off
2021-05-11 23:30:32 [DEBUG] Loading ..99%
2021-05-11 23:30:32 [DEBUG] INFO- Loaded 126108 vertices and 252216 faces.
2021-05-11 23:30:39 [DEBUG] 0% done
2021-05-11 23:30:39 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:30:39 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-11 23:30:39 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:30:39 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:30:39 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:31:02 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:31:02 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.269019 (15.413659 DEGs)
2021-05-11 23:31:02 [DEBUG] INFO- *** Triangulation Report ***
2021-05-11 23:31:02 [DEBUG] INFO- V: 126108
2021-05-11 23:31:02 [DEBUG] INFO- E: 378324
2021-05-11 23:31:02 [DEBUG] INFO- T: 252216
2021-05-11 23:31:02 [DEBUG] INFO- Boundary: 0 components.
2021-05-11 23:31:02 [DEBUG] INFO- Handles: 1.
2021-05-11 23:31:02 [DEBUG] INFO- Shells: 1.
2021-05-11 23:31:02 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off'
2021-05-11 23:31:02 [INFO ] Voxelizing gray matter
2021-05-11 23:31:02 [DEBUG] Creating gmx.nii.gz from gmx.off
2021-05-11 23:31:06 [DEBUG] Making splits in z direction, tracing in x
2021-05-11 23:35:39 [INFO ] Decoupling volumes
2021-05-11 23:35:42 [INFO ] Surface extraction: white matter
2021-05-11 23:35:42 [DEBUG] Generating surface mesh from wmx.nii.gz
2021-05-11 23:35:42 [DEBUG] Creating initial mesh
2021-05-11 23:35:55 [DEBUG] Keeping maximum 1 largest shell(s) with minimum area of 1
2021-05-11 23:35:55 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx_mesh.off" -a 2.0 --no-clean -q --shells 1 --splitShells --shellMinArea 1 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii"
2021-05-11 23:36:28 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:36:28 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx_mesh.off
2021-05-11 23:36:28 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-11 23:36:29 [DEBUG] Processing wmx.nii1.off
2021-05-11 23:36:29 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.stl"
2021-05-11 23:36:29 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-11 23:36:40 [DEBUG] Loading ..101%
2021-05-11 23:36:40 [DEBUG] INFO- Loaded 379083 vertices and 769454 faces.
2021-05-11 23:38:38 [DEBUG] 0% done
2021-05-11 23:38:38 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.stl'
2021-05-11 23:38:38 [DEBUG] Resampling to a vertex density of 0.5
2021-05-11 23:38:38 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off"
2021-05-11 23:51:02 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:51:02 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-11 23:51:02 [DEBUG] Uniform remeshing ...
2021-05-11 23:51:02 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:51:02 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off'
2021-05-11 23:51:02 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1_resampled.stl"
2021-05-11 23:51:03 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-11 23:51:07 [DEBUG] Loading ..100%
2021-05-11 23:51:07 [DEBUG] INFO- Loaded 152533 vertices and 307034 faces.
2021-05-11 23:51:53 [DEBUG] 0% done
2021-05-11 23:51:53 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1_resampled.stl'
2021-05-11 23:51:53 [DEBUG] Cleaning
2021-05-11 23:51:53 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off"
2021-05-11 23:52:40 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:52:40 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-11 23:52:40 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:52:40 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off'
2021-05-11 23:52:40 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1_resampled_clean.stl"
2021-05-11 23:52:40 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-11 23:52:45 [DEBUG] Loading ..100%
2021-05-11 23:52:45 [DEBUG] INFO- Loaded 152533 vertices and 307034 faces.
2021-05-11 23:53:31 [DEBUG] 0% done
2021-05-11 23:53:31 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1_resampled_clean.stl'
2021-05-11 23:53:31 [DEBUG] Smoothing 5 time(s)
2021-05-11 23:53:31 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off"
2021-05-11 23:53:31 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:53:31 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-11 23:53:36 [DEBUG] Loading ..100%
2021-05-11 23:53:36 [DEBUG] INFO- Loaded 152533 vertices and 307034 faces.
2021-05-11 23:53:36 [DEBUG] 0% done
2021-05-11 23:53:36 [DEBUG] Smoothing 5 steps.
2021-05-11 23:53:36 [DEBUG] INFO- Lambda: 0.500000
2021-05-11 23:54:25 [DEBUG] 99 % done - 1 steps left
2021-05-11 23:54:25 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off'
2021-05-11 23:54:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1_resampled_clean_smoothed.stl"
2021-05-11 23:54:25 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-11 23:54:30 [DEBUG] Loading ..100%
2021-05-11 23:54:30 [DEBUG] INFO- Loaded 152533 vertices and 307034 faces.
2021-05-11 23:55:17 [DEBUG] 0% done
2021-05-11 23:55:17 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1_resampled_clean_smoothed.stl'
2021-05-11 23:55:17 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-11 23:55:17 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-11 23:55:17 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-11 23:55:17 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-11 23:55:17 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-11 23:55:23 [DEBUG] Loading ..100%
2021-05-11 23:55:23 [DEBUG] INFO- Loaded 152533 vertices and 307034 faces.
2021-05-11 23:55:28 [DEBUG] 0% done
2021-05-11 23:55:28 [DEBUG] Removing Spikes.
2021-05-11 23:55:28 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-11 23:55:28 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-11 23:55:28 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:55:40 [DEBUG] INFO- Removed the smallest 1 of 2 shells
2021-05-11 23:55:50 [DEBUG] INFO- Removed the smallest 2 of 3 shells
2021-05-11 23:56:04 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:56:04 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:56:21 [DEBUG] INFO- 142 intersecting triangles have been selected (in selection).
2021-05-11 23:56:28 [DEBUG] INFO- 20 intersecting triangles have been selected (in selection).
2021-05-11 23:56:35 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:57:03 [DEBUG] INFO- No intersecting triangles detected.
2021-05-11 23:57:03 [DEBUG] INFO- *** Cleaning iteration 1 ***
2021-05-11 23:57:03 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:57:03 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:57:03 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:57:20 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:57:30 [DEBUG] 100% done
2021-05-11 23:57:30 [DEBUG] INFO- *** Cleaning iteration 2 ***
2021-05-11 23:57:30 [DEBUG] INFO- Removing degeneracies...
2021-05-11 23:57:30 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-11 23:57:30 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-11 23:58:06 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-11 23:58:06 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.272268 (15.599804 DEGs)
2021-05-11 23:58:06 [DEBUG] INFO- *** Triangulation Report ***
2021-05-11 23:58:06 [DEBUG] INFO- V: 150954
2021-05-11 23:58:06 [DEBUG] INFO- E: 455496
2021-05-11 23:58:06 [DEBUG] INFO- T: 303664
2021-05-11 23:58:06 [DEBUG] INFO- Boundary: 0 components.
2021-05-11 23:58:06 [DEBUG] INFO- Handles: 440.
2021-05-11 23:58:06 [DEBUG] INFO- Shells: 1.
2021-05-11 23:58:06 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-11 23:58:06 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1_resampled_clean_smoothed_spike.stl"
2021-05-11 23:58:07 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-11 23:58:12 [DEBUG] Loading ..100%
2021-05-11 23:58:12 [DEBUG] INFO- Loaded 152533 vertices and 307034 faces.
2021-05-11 23:59:00 [DEBUG] 0% done
2021-05-11 23:59:00 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1_resampled_clean_smoothed_spike.stl'
2021-05-11 23:59:00 [DEBUG] Uniform remeshing
2021-05-11 23:59:00 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off"
2021-05-12 00:06:44 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:06:44 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-12 00:06:44 [DEBUG] Uniform remeshing ...
2021-05-12 00:06:44 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:06:44 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off'
2021-05-12 00:06:44 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 00:06:45 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-12 00:06:49 [DEBUG] Loading ..100%
2021-05-12 00:06:49 [DEBUG] INFO- Loaded 152101 vertices and 305882 faces.
2021-05-12 00:07:35 [DEBUG] 0% done
2021-05-12 00:07:35 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 00:07:35 [DEBUG] Cleaning
2021-05-12 00:07:35 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off"
2021-05-12 00:08:16 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:08:16 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-12 00:08:16 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:08:16 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off'
2021-05-12 00:08:59 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off"
2021-05-12 00:14:05 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:14:05 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-12 00:14:05 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:14:05 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off'
2021-05-12 00:14:05 [INFO ] Surface extraction: ventricle
2021-05-12 00:14:05 [DEBUG] Generating surface mesh from ventricles.nii.gz
2021-05-12 00:14:05 [DEBUG] Creating initial mesh
2021-05-12 00:14:07 [DEBUG] Keeping maximum 5 largest shell(s) with minimum area of 200
2021-05-12 00:14:07 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles_mesh.off" -a 2.0 --no-clean -q --shells 5 --splitShells --shellMinArea 200 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii"
2021-05-12 00:14:08 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:14:08 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles_mesh.off
2021-05-12 00:14:08 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:08 [DEBUG] Processing ventricles.nii1.off
2021-05-12 00:14:08 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.stl"
2021-05-12 00:14:08 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:09 [DEBUG] Loading ..98%
2021-05-12 00:14:09 [DEBUG] INFO- Loaded 17243 vertices and 34742 faces.
2021-05-12 00:14:14 [DEBUG] 0% done
2021-05-12 00:14:14 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.stl'
2021-05-12 00:14:14 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 00:14:14 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off"
2021-05-12 00:14:27 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:14:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:27 [DEBUG] Uniform remeshing ...
2021-05-12 00:14:27 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:14:27 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off'
2021-05-12 00:14:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1_resampled.stl"
2021-05-12 00:14:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:27 [DEBUG] Loading ..96%
2021-05-12 00:14:27 [DEBUG] INFO- Loaded 7248 vertices and 14536 faces.
2021-05-12 00:14:29 [DEBUG] 0% done
2021-05-12 00:14:29 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1_resampled.stl'
2021-05-12 00:14:29 [DEBUG] Cleaning
2021-05-12 00:14:29 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off"
2021-05-12 00:14:31 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:14:31 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:31 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:14:31 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off'
2021-05-12 00:14:31 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1_resampled_clean.stl"
2021-05-12 00:14:31 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:31 [DEBUG] Loading ..96%
2021-05-12 00:14:31 [DEBUG] INFO- Loaded 7248 vertices and 14536 faces.
2021-05-12 00:14:34 [DEBUG] 0% done
2021-05-12 00:14:34 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1_resampled_clean.stl'
2021-05-12 00:14:34 [DEBUG] Smoothing 5 time(s)
2021-05-12 00:14:34 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off"
2021-05-12 00:14:34 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:14:34 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:34 [DEBUG] Loading ..96%
2021-05-12 00:14:34 [DEBUG] INFO- Loaded 7248 vertices and 14536 faces.
2021-05-12 00:14:34 [DEBUG] 0% done
2021-05-12 00:14:34 [DEBUG] Smoothing 5 steps.
2021-05-12 00:14:34 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 00:14:36 [DEBUG] 99 % done - 1 steps left
2021-05-12 00:14:36 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off'
2021-05-12 00:14:36 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1_resampled_clean_smoothed.stl"
2021-05-12 00:14:37 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:37 [DEBUG] Loading ..96%
2021-05-12 00:14:37 [DEBUG] INFO- Loaded 7248 vertices and 14536 faces.
2021-05-12 00:14:39 [DEBUG] 0% done
2021-05-12 00:14:39 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1_resampled_clean_smoothed.stl'
2021-05-12 00:14:39 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 00:14:39 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:39 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:14:39 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 00:14:39 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:39 [DEBUG] Loading ..96%
2021-05-12 00:14:39 [DEBUG] INFO- Loaded 7248 vertices and 14536 faces.
2021-05-12 00:14:40 [DEBUG] 0% done
2021-05-12 00:14:40 [DEBUG] Removing Spikes.
2021-05-12 00:14:40 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:14:40 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 00:14:40 [DEBUG] INFO- Removing degeneracies...
2021-05-12 00:14:40 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 00:14:40 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 00:14:40 [DEBUG] INFO- 5 intersecting triangles have been selected (in selection).
2021-05-12 00:14:41 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 00:14:42 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:14:42 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.323524 (18.536546 DEGs)
2021-05-12 00:14:42 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 00:14:42 [DEBUG] INFO- V: 7226
2021-05-12 00:14:42 [DEBUG] INFO- E: 21738
2021-05-12 00:14:42 [DEBUG] INFO- T: 14492
2021-05-12 00:14:42 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 00:14:42 [DEBUG] INFO- Handles: 11.
2021-05-12 00:14:42 [DEBUG] INFO- Shells: 1.
2021-05-12 00:14:42 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 00:14:42 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1_resampled_clean_smoothed_spike.stl"
2021-05-12 00:14:42 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:42 [DEBUG] Loading ..96%
2021-05-12 00:14:42 [DEBUG] INFO- Loaded 7248 vertices and 14536 faces.
2021-05-12 00:14:44 [DEBUG] 0% done
2021-05-12 00:14:44 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1_resampled_clean_smoothed_spike.stl'
2021-05-12 00:14:44 [DEBUG] Uniform remeshing
2021-05-12 00:14:44 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off"
2021-05-12 00:14:46 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:14:46 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:46 [DEBUG] Uniform remeshing ...
2021-05-12 00:14:46 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:14:46 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off'
2021-05-12 00:14:46 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 00:14:47 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:47 [DEBUG] Loading ..96%
2021-05-12 00:14:47 [DEBUG] INFO- Loaded 7243 vertices and 14522 faces.
2021-05-12 00:14:49 [DEBUG] 0% done
2021-05-12 00:14:49 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 00:14:49 [DEBUG] Cleaning
2021-05-12 00:14:49 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off"
2021-05-12 00:14:51 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:14:51 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:51 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:14:51 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off'
2021-05-12 00:14:53 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off"
2021-05-12 00:14:55 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:14:55 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:55 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:14:55 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off'
2021-05-12 00:14:55 [INFO ] Decoupling surfaces
2021-05-12 00:14:55 [INFO ] Decoupling ventricles.nii1 from GM
2021-05-12 00:14:55 [DEBUG] Decoupling VENTRICLES.NII1.OFF (inner surface) from GMX.OFF (outer surface)
2021-05-12 00:14:55 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" --shells 2 --no-clean --intersect
2021-05-12 00:14:56 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:14:56 [DEBUG] Loading ..98%
2021-05-12 00:14:56 [DEBUG] INFO- Loaded 7085 vertices and 14202 faces.
2021-05-12 00:15:00 [DEBUG] Loading ..99%
2021-05-12 00:15:00 [DEBUG] INFO- Loaded 126108 vertices and 252216 faces.
2021-05-12 00:15:00 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off was joined.
2021-05-12 00:15:00 [DEBUG] 0% done
2021-05-12 00:15:00 [DEBUG] Testing for intersections ...
2021-05-12 00:15:15 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:15:15 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" --shells 2 --no-clean --intersect
2021-05-12 00:15:15 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:15:15 [DEBUG] Loading ..98%
2021-05-12 00:15:15 [DEBUG] INFO- Loaded 7085 vertices and 14202 faces.
2021-05-12 00:15:19 [DEBUG] Loading ..99%
2021-05-12 00:15:19 [DEBUG] INFO- Loaded 126108 vertices and 252216 faces.
2021-05-12 00:15:19 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off was joined.
2021-05-12 00:15:19 [DEBUG] 0% done
2021-05-12 00:15:19 [DEBUG] Testing for intersections ...
2021-05-12 00:15:34 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:15:34 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking VENTRICLES.NII1.OFF (inner surface)
2021-05-12 00:15:39 [DEBUG] Cleaning VENTRICLES.NII1.OFF (inner surface)
2021-05-12 00:15:39 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off"
2021-05-12 00:15:43 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:15:43 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:15:43 [DEBUG] Uniform remeshing ...
2021-05-12 00:15:43 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:15:43 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off'
2021-05-12 00:15:43 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off"
2021-05-12 00:15:45 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:15:45 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:15:45 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:15:45 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off'
2021-05-12 00:15:45 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" --shells 2 --no-clean --intersect
2021-05-12 00:15:45 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:15:45 [DEBUG] Loading ..98%
2021-05-12 00:15:45 [DEBUG] INFO- Loaded 7084 vertices and 14200 faces.
2021-05-12 00:15:49 [DEBUG] Loading ..99%
2021-05-12 00:15:49 [DEBUG] INFO- Loaded 126108 vertices and 252216 faces.
2021-05-12 00:15:49 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off was joined.
2021-05-12 00:15:49 [DEBUG] 0% done
2021-05-12 00:15:49 [DEBUG] Testing for intersections ...
2021-05-12 00:16:04 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:16:04 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 00:16:04 [INFO ] Decoupling WM from ventricles.nii1
2021-05-12 00:16:04 [DEBUG] Decoupling WMX.NII1.OFF (surface 1) from VENTRICLES.NII1.OFF (surface 2)
2021-05-12 00:16:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" --shells 2 --no-clean --intersect
2021-05-12 00:16:05 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-12 00:16:10 [DEBUG] Loading ..100%
2021-05-12 00:16:10 [DEBUG] INFO- Loaded 150918 vertices and 303048 faces.
2021-05-12 00:16:10 [DEBUG] Loading ..98%
2021-05-12 00:16:10 [DEBUG] INFO- Loaded 7084 vertices and 14200 faces.
2021-05-12 00:16:10 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off was joined.
2021-05-12 00:16:10 [DEBUG] 0% done
2021-05-12 00:16:10 [DEBUG] Testing for intersections ...
2021-05-12 00:16:30 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:16:30 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" --shells 2 --no-clean --intersect
2021-05-12 00:16:31 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-12 00:16:36 [DEBUG] Loading ..100%
2021-05-12 00:16:36 [DEBUG] INFO- Loaded 150918 vertices and 303048 faces.
2021-05-12 00:16:37 [DEBUG] Loading ..98%
2021-05-12 00:16:37 [DEBUG] INFO- Loaded 7084 vertices and 14200 faces.
2021-05-12 00:16:37 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off was joined.
2021-05-12 00:16:37 [DEBUG] 0% done
2021-05-12 00:16:37 [DEBUG] Testing for intersections ...
2021-05-12 00:16:55 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:16:55 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking WMX.NII1.OFF (surface 1)
2021-05-12 00:17:07 [DEBUG] Moved 10.0 of 150918 vertices
2021-05-12 00:17:11 [DEBUG] Cleaning WMX.NII1.OFF (surface 1)
2021-05-12 00:17:11 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off"
2021-05-12 00:23:10 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:23:10 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-12 00:23:10 [DEBUG] Uniform remeshing ...
2021-05-12 00:23:10 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:23:10 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off'
2021-05-12 00:23:10 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off"
2021-05-12 00:23:52 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:23:52 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-12 00:23:52 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:23:52 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off'
2021-05-12 00:23:52 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" --shells 2 --no-clean --intersect
2021-05-12 00:23:52 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-12 00:23:57 [DEBUG] Loading ..100%
2021-05-12 00:23:57 [DEBUG] INFO- Loaded 150687 vertices and 302478 faces.
2021-05-12 00:23:57 [DEBUG] Loading ..98%
2021-05-12 00:23:57 [DEBUG] INFO- Loaded 7084 vertices and 14200 faces.
2021-05-12 00:23:57 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off was joined.
2021-05-12 00:23:58 [DEBUG] 0% done
2021-05-12 00:23:58 [DEBUG] Testing for intersections ...
2021-05-12 00:24:16 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:24:16 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 00:24:16 [INFO ] Decoupling GM from WM
2021-05-12 00:24:16 [DEBUG] Decoupling GMX.OFF (outer surface) from WMX.NII1.OFF (inner surface)
2021-05-12 00:24:16 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --shells 2 --no-clean --intersect
2021-05-12 00:24:16 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off
2021-05-12 00:24:20 [DEBUG] Loading ..99%
2021-05-12 00:24:20 [DEBUG] INFO- Loaded 126108 vertices and 252216 faces.
2021-05-12 00:24:25 [DEBUG] Loading ..100%
2021-05-12 00:24:25 [DEBUG] INFO- Loaded 150687 vertices and 302478 faces.
2021-05-12 00:24:25 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off was joined.
2021-05-12 00:24:25 [DEBUG] 0% done
2021-05-12 00:24:25 [DEBUG] Testing for intersections ...
2021-05-12 00:25:18 [DEBUG] INFO- 96 intersecting triangles have been selected.
2021-05-12 00:25:18 [DEBUG] Iteration 1
2021-05-12 00:25:18 [DEBUG] Decoupling
2021-05-12 00:25:18 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" -a 2.0 --shells 2 --decouple-outout 0 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off"
2021-05-12 00:25:19 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:25:19 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off
2021-05-12 00:25:22 [DEBUG] Loading ..99%
2021-05-12 00:25:22 [DEBUG] INFO- Loaded 126108 vertices and 252216 faces.
2021-05-12 00:25:28 [DEBUG] Loading ..100%
2021-05-12 00:25:28 [DEBUG] INFO- Loaded 150687 vertices and 302478 faces.
2021-05-12 00:25:28 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off was joined.
2021-05-12 00:26:06 [DEBUG] 0% done
2021-05-12 00:26:06 [DEBUG] Decoupling first (outer) component from second one (move outwards). Min. distance: 0.
2021-05-12 00:26:06 [DEBUG] INFO- Iteration 1
2021-05-12 00:27:13 [DEBUG] INFO- 96 intersecting triangles have been selected.
2021-05-12 00:27:18 [DEBUG] INFO- Number of triangles inside: 56
2021-05-12 00:28:34 [DEBUG] INFO- Iteration 2
2021-05-12 00:28:44 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 00:28:55 [DEBUG] INFO- Number of triangles inside: 0
2021-05-12 00:28:55 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:28:55 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 00:28:55 [DEBUG] INFO- Removing degeneracies...
2021-05-12 00:28:55 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 00:28:55 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 00:29:18 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 00:29:18 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.269019 (15.413659 DEGs)
2021-05-12 00:29:18 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 00:29:18 [DEBUG] INFO- V: 126089
2021-05-12 00:29:18 [DEBUG] INFO- E: 378267
2021-05-12 00:29:18 [DEBUG] INFO- T: 252178
2021-05-12 00:29:18 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 00:29:18 [DEBUG] INFO- Handles: 1.
2021-05-12 00:29:18 [DEBUG] INFO- Shells: 1.
2021-05-12 00:29:18 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off'
2021-05-12 00:29:18 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --shells 2 --no-clean --intersect
2021-05-12 00:29:18 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off
2021-05-12 00:29:21 [DEBUG] Loading ..99%
2021-05-12 00:29:21 [DEBUG] INFO- Loaded 126089 vertices and 252178 faces.
2021-05-12 00:29:26 [DEBUG] Loading ..100%
2021-05-12 00:29:26 [DEBUG] INFO- Loaded 150687 vertices and 302478 faces.
2021-05-12 00:29:26 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off was joined.
2021-05-12 00:29:27 [DEBUG] 0% done
2021-05-12 00:29:27 [DEBUG] Testing for intersections ...
2021-05-12 00:30:18 [DEBUG] INFO- 13 intersecting triangles have been selected.
2021-05-12 00:30:18 [DEBUG] Decoupling
2021-05-12 00:30:18 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" -a 2.0 --shells 2 --decouple-outout 0 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off"
2021-05-12 00:30:19 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:30:19 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off
2021-05-12 00:30:22 [DEBUG] Loading ..99%
2021-05-12 00:30:22 [DEBUG] INFO- Loaded 126089 vertices and 252178 faces.
2021-05-12 00:30:27 [DEBUG] Loading ..100%
2021-05-12 00:30:27 [DEBUG] INFO- Loaded 150687 vertices and 302478 faces.
2021-05-12 00:30:27 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off was joined.
2021-05-12 00:31:01 [DEBUG] 0% done
2021-05-12 00:31:01 [DEBUG] Decoupling first (outer) component from second one (move outwards). Min. distance: 0.
2021-05-12 00:31:01 [DEBUG] INFO- Iteration 1
2021-05-12 00:31:57 [DEBUG] INFO- 13 intersecting triangles have been selected.
2021-05-12 00:32:01 [DEBUG] INFO- Number of triangles inside: 7
2021-05-12 00:32:52 [DEBUG] INFO- Iteration 2
2021-05-12 00:33:52 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:34:02 [DEBUG] INFO- Number of triangles inside: 0
2021-05-12 00:34:02 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:34:02 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 00:34:02 [DEBUG] INFO- Removing degeneracies...
2021-05-12 00:34:02 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 00:34:02 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 00:34:27 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 00:34:27 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.269019 (15.413659 DEGs)
2021-05-12 00:34:27 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 00:34:27 [DEBUG] INFO- V: 126084
2021-05-12 00:34:27 [DEBUG] INFO- E: 378252
2021-05-12 00:34:27 [DEBUG] INFO- T: 252168
2021-05-12 00:34:27 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 00:34:27 [DEBUG] INFO- Handles: 1.
2021-05-12 00:34:27 [DEBUG] INFO- Shells: 1.
2021-05-12 00:34:27 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off'
2021-05-12 00:34:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --shells 2 --no-clean --intersect
2021-05-12 00:34:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off
2021-05-12 00:34:31 [DEBUG] Loading ..99%
2021-05-12 00:34:31 [DEBUG] INFO- Loaded 126084 vertices and 252168 faces.
2021-05-12 00:34:36 [DEBUG] Loading ..100%
2021-05-12 00:34:36 [DEBUG] INFO- Loaded 150687 vertices and 302478 faces.
2021-05-12 00:34:36 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off was joined.
2021-05-12 00:34:36 [DEBUG] 0% done
2021-05-12 00:34:36 [DEBUG] Testing for intersections ...
2021-05-12 00:35:25 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:35:25 [DEBUG] Cutting GMX.OFF (outer surface)
2021-05-12 00:35:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" -a 2.0 --shells 2 --cut-inner 0 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off"
2021-05-12 00:35:26 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:35:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off
2021-05-12 00:35:29 [DEBUG] Loading ..99%
2021-05-12 00:35:29 [DEBUG] INFO- Loaded 126084 vertices and 252168 faces.
2021-05-12 00:35:34 [DEBUG] Loading ..100%
2021-05-12 00:35:34 [DEBUG] INFO- Loaded 150687 vertices and 302478 faces.
2021-05-12 00:35:34 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off was joined.
2021-05-12 00:36:08 [DEBUG] 0% done
2021-05-12 00:36:08 [DEBUG] Cutting triangles of the first component away, that are inside of the second one; Fill holes.
2021-05-12 00:37:08 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:37:21 [DEBUG] INFO- Number of triangles inside: 0
2021-05-12 00:37:21 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 00:37:21 [DEBUG] INFO- V: 126084
2021-05-12 00:37:21 [DEBUG] INFO- E: 378252
2021-05-12 00:37:21 [DEBUG] INFO- T: 252168
2021-05-12 00:37:21 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 00:37:21 [DEBUG] INFO- Handles: 1.
2021-05-12 00:37:21 [DEBUG] INFO- Shells: 1.
2021-05-12 00:37:21 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 00:37:21 [DEBUG] INFO- Removing degeneracies...
2021-05-12 00:37:21 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 00:37:21 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 00:37:48 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 00:37:48 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.269019 (15.413659 DEGs)
2021-05-12 00:37:48 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 00:37:48 [DEBUG] INFO- V: 126084
2021-05-12 00:37:48 [DEBUG] INFO- E: 378252
2021-05-12 00:37:48 [DEBUG] INFO- T: 252168
2021-05-12 00:37:48 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 00:37:48 [DEBUG] INFO- Handles: 1.
2021-05-12 00:37:48 [DEBUG] INFO- Shells: 1.
2021-05-12 00:37:48 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:37:48 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 00:37:48 [DEBUG] INFO- Removing degeneracies...
2021-05-12 00:37:48 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 00:37:48 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 00:38:10 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 00:38:10 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.269019 (15.413659 DEGs)
2021-05-12 00:38:10 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 00:38:10 [DEBUG] INFO- V: 126084
2021-05-12 00:38:10 [DEBUG] INFO- E: 378252
2021-05-12 00:38:10 [DEBUG] INFO- T: 252168
2021-05-12 00:38:10 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 00:38:10 [DEBUG] INFO- Handles: 1.
2021-05-12 00:38:10 [DEBUG] INFO- Shells: 1.
2021-05-12 00:38:10 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off'
2021-05-12 00:38:10 [DEBUG] Cleaning GMX.OFF (outer surface)
2021-05-12 00:38:10 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off"
2021-05-12 00:40:29 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:40:29 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off
2021-05-12 00:40:29 [DEBUG] Uniform remeshing ...
2021-05-12 00:40:29 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:40:29 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off'
2021-05-12 00:40:29 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off"
2021-05-12 00:41:03 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:41:03 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off
2021-05-12 00:41:03 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:41:03 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off'
2021-05-12 00:41:03 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --shells 2 --no-clean --intersect
2021-05-12 00:41:03 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off
2021-05-12 00:41:07 [DEBUG] Loading ..99%
2021-05-12 00:41:07 [DEBUG] INFO- Loaded 126022 vertices and 252044 faces.
2021-05-12 00:41:12 [DEBUG] Loading ..100%
2021-05-12 00:41:12 [DEBUG] INFO- Loaded 150687 vertices and 302478 faces.
2021-05-12 00:41:12 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off was joined.
2021-05-12 00:41:12 [DEBUG] 0% done
2021-05-12 00:41:12 [DEBUG] Testing for intersections ...
2021-05-12 00:41:58 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:41:58 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --shells 2 --no-clean --intersect
2021-05-12 00:41:59 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off
2021-05-12 00:42:02 [DEBUG] Loading ..99%
2021-05-12 00:42:02 [DEBUG] INFO- Loaded 126022 vertices and 252044 faces.
2021-05-12 00:42:07 [DEBUG] Loading ..100%
2021-05-12 00:42:07 [DEBUG] INFO- Loaded 150687 vertices and 302478 faces.
2021-05-12 00:42:07 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off was joined.
2021-05-12 00:42:08 [DEBUG] 0% done
2021-05-12 00:42:08 [DEBUG] Testing for intersections ...
2021-05-12 00:42:54 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:42:54 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --shells 2 --no-clean --intersect
2021-05-12 00:42:54 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off
2021-05-12 00:42:57 [DEBUG] Loading ..99%
2021-05-12 00:42:57 [DEBUG] INFO- Loaded 126022 vertices and 252044 faces.
2021-05-12 00:43:02 [DEBUG] Loading ..100%
2021-05-12 00:43:02 [DEBUG] INFO- Loaded 150687 vertices and 302478 faces.
2021-05-12 00:43:02 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off was joined.
2021-05-12 00:43:03 [DEBUG] 0% done
2021-05-12 00:43:03 [DEBUG] Testing for intersections ...
2021-05-12 00:43:49 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:43:49 [DEBUG] Total iterations needed for decoupling: 1
2021-05-12 00:43:49 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --shells 2 --no-clean -q --intersect
2021-05-12 00:44:13 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:44:13 [DEBUG] Testing for intersections ...
2021-05-12 00:44:13 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" --shells 2 --no-clean -q --intersect
2021-05-12 00:44:32 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:44:32 [DEBUG] Testing for intersections ...
2021-05-12 00:44:32 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" --shells 2 --no-clean -q --intersect
2021-05-12 00:45:28 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-12 00:45:28 [DEBUG] Testing for intersections ...
2021-05-12 00:45:28 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" --shells 2 --no-clean -q --intersect
2021-05-12 00:45:51 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:45:51 [DEBUG] Testing for intersections ...
2021-05-12 00:45:51 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" --shells 2 --no-clean -q --intersect
2021-05-12 00:46:10 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\ventricles.nii1.off
2021-05-12 00:46:10 [DEBUG] Testing for intersections ...
2021-05-12 00:46:10 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\gmx.off" --shells 2 --no-clean -q --intersect
2021-05-12 00:47:06 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\wmx.nii1.off
2021-05-12 00:47:06 [DEBUG] Testing for intersections ...
2021-05-12 00:47:06 [INFO ] Voxelizing white matter
2021-05-12 00:47:06 [DEBUG] Creating cat_surf_wm.nii.gz from cat_surf_wm.off
2021-05-12 00:47:10 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 00:52:06 [INFO ] Voxelizing ventricles
2021-05-12 00:52:06 [DEBUG] Creating cat_surf_ventricles.nii1.nii.gz from cat_surf_ventricles.nii1.off
2021-05-12 00:52:07 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 00:52:24 [DEBUG] Creating cat_surf_ventricles.nii1.nii.gz from cat_surf_ventricles.nii1.off
2021-05-12 00:52:24 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 00:52:41 [INFO ] ========================================================================
2021-05-12 00:52:41 [INFO ] CAT preparation time: 01:55:29
2021-05-12 00:52:41 [INFO ] ========================================================================
2021-05-12 00:52:41 [INFO ] CLEANING SEGMENTATIONS
2021-05-12 00:52:41 [INFO ] ========================================================================
2021-05-12 00:52:43 [INFO ] Cleaning bone
2021-05-12 00:52:45 [INFO ] Cleaning skin
2021-05-12 00:52:47 [INFO ] Cleaning CSF
2021-05-12 00:52:48 [INFO ] Cleaning WM
2021-05-12 00:52:48 [INFO ] Labelling unassigned voxels (protecting everything inside GM mask from CAT)
2021-05-12 00:53:08 [INFO ] Constructing outer tissue surfaces
2021-05-12 00:53:08 [INFO ] White matter
2021-05-12 00:53:08 [INFO ] Gray matter
2021-05-12 00:53:08 [INFO ] CSF and eyes
2021-05-12 00:53:16 [INFO ] Ventricles
2021-05-12 00:53:17 [INFO ] Bone
2021-05-12 00:53:22 [INFO ] Skin
2021-05-12 00:53:26 [INFO ] Air
2021-05-12 00:53:31 [INFO ] Ensuring tissue masks are properly contained within each other
2021-05-12 00:53:32 [INFO ] # voxels removed from bone : 195
2021-05-12 00:53:33 [INFO ] Saving individual tissue masks
2021-05-12 00:53:34 [INFO ] Saving combined tissue mask
2021-05-12 00:53:37 [INFO ] ========================================================================
2021-05-12 00:53:37 [INFO ] Cleaning time: 00:00:56
2021-05-12 00:53:37 [INFO ] ========================================================================
2021-05-12 00:53:37 [INFO ] GENERATING SURFACE MESHES
2021-05-12 00:53:37 [INFO ] ========================================================================
2021-05-12 00:53:37 [INFO ] Processing WM
2021-05-12 00:53:37 [INFO ] ========================================================================
2021-05-12 00:53:37 [INFO ] Fetching previously created files
2021-05-12 00:53:37 [INFO ] WM processing time: 00:00:00
2021-05-12 00:53:37 [INFO ] Processing GM
2021-05-12 00:53:37 [INFO ] ========================================================================
2021-05-12 00:53:37 [INFO ] Fetching previously created files
2021-05-12 00:53:37 [INFO ] GM processing time: 00:00:00
2021-05-12 00:53:37 [INFO ] Processing CSF
2021-05-12 00:53:37 [INFO ] ========================================================================
2021-05-12 00:53:37 [INFO ] Preparing volume for meshing
2021-05-12 00:53:40 [INFO ] Extracting surface
2021-05-12 00:53:40 [DEBUG] Generating surface mesh from mod_csf.nii.gz
2021-05-12 00:53:40 [DEBUG] Creating initial mesh
2021-05-12 00:53:44 [DEBUG] Keeping maximum 1 largest shell(s) with minimum area of 1
2021-05-12 00:53:44 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\mod_csf_mesh.off" -a 2.0 --no-clean -q --shells 1 --splitShells --shellMinArea 1 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf"
2021-05-12 00:53:54 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:53:54 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\mod_csf_mesh.off
2021-05-12 00:53:54 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:53:54 [DEBUG] Processing fixed_csf1.off
2021-05-12 00:53:54 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.stl"
2021-05-12 00:53:54 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:53:57 [DEBUG] Loading ..99%
2021-05-12 00:53:57 [DEBUG] INFO- Loaded 117644 vertices and 235344 faces.
2021-05-12 00:54:30 [DEBUG] 0% done
2021-05-12 00:54:30 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.stl'
2021-05-12 00:54:30 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 00:54:30 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off"
2021-05-12 00:55:15 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:55:15 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:55:15 [DEBUG] Uniform remeshing ...
2021-05-12 00:55:15 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:55:15 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off'
2021-05-12 00:55:15 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1_resampled.stl"
2021-05-12 00:55:15 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:55:17 [DEBUG] Loading ..99%
2021-05-12 00:55:17 [DEBUG] INFO- Loaded 48123 vertices and 96242 faces.
2021-05-12 00:55:31 [DEBUG] 0% done
2021-05-12 00:55:31 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1_resampled.stl'
2021-05-12 00:55:31 [DEBUG] Cleaning
2021-05-12 00:55:31 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off"
2021-05-12 00:55:39 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:55:39 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:55:39 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:55:39 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off'
2021-05-12 00:55:39 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1_resampled_clean.stl"
2021-05-12 00:55:39 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:55:41 [DEBUG] Loading ..99%
2021-05-12 00:55:41 [DEBUG] INFO- Loaded 48123 vertices and 96242 faces.
2021-05-12 00:55:55 [DEBUG] 0% done
2021-05-12 00:55:55 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1_resampled_clean.stl'
2021-05-12 00:55:55 [DEBUG] Smoothing 5 time(s)
2021-05-12 00:55:55 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off"
2021-05-12 00:55:55 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:55:55 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:55:57 [DEBUG] Loading ..99%
2021-05-12 00:55:57 [DEBUG] INFO- Loaded 48123 vertices and 96242 faces.
2021-05-12 00:55:57 [DEBUG] 0% done
2021-05-12 00:55:57 [DEBUG] Smoothing 5 steps.
2021-05-12 00:55:57 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 00:56:11 [DEBUG] 99 % done - 1 steps left
2021-05-12 00:56:11 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off'
2021-05-12 00:56:11 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1_resampled_clean_smoothed.stl"
2021-05-12 00:56:11 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:56:13 [DEBUG] Loading ..99%
2021-05-12 00:56:13 [DEBUG] INFO- Loaded 48123 vertices and 96242 faces.
2021-05-12 00:56:27 [DEBUG] 0% done
2021-05-12 00:56:27 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1_resampled_clean_smoothed.stl'
2021-05-12 00:56:27 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 00:56:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:56:27 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:56:27 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 00:56:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:56:28 [DEBUG] Loading ..99%
2021-05-12 00:56:28 [DEBUG] INFO- Loaded 48123 vertices and 96242 faces.
2021-05-12 00:56:31 [DEBUG] 0% done
2021-05-12 00:56:31 [DEBUG] Removing Spikes.
2021-05-12 00:56:31 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:56:31 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 00:56:31 [DEBUG] INFO- Removing degeneracies...
2021-05-12 00:56:31 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 00:56:31 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 00:56:33 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 00:56:36 [DEBUG] 100% done
2021-05-12 00:56:36 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 1.113527 (63.800388 DEGs)
2021-05-12 00:56:36 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 00:56:36 [DEBUG] INFO- V: 48101
2021-05-12 00:56:36 [DEBUG] INFO- E: 144297
2021-05-12 00:56:36 [DEBUG] INFO- T: 96198
2021-05-12 00:56:36 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 00:56:36 [DEBUG] INFO- Handles: 0.
2021-05-12 00:56:36 [DEBUG] INFO- Shells: 1.
2021-05-12 00:56:36 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 00:56:36 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1_resampled_clean_smoothed_spike.stl"
2021-05-12 00:56:37 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:56:38 [DEBUG] Loading ..99%
2021-05-12 00:56:38 [DEBUG] INFO- Loaded 48123 vertices and 96242 faces.
2021-05-12 00:56:53 [DEBUG] 0% done
2021-05-12 00:56:53 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1_resampled_clean_smoothed_spike.stl'
2021-05-12 00:56:53 [DEBUG] Uniform remeshing
2021-05-12 00:56:53 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off"
2021-05-12 00:57:04 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:57:04 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:57:04 [DEBUG] Uniform remeshing ...
2021-05-12 00:57:04 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:57:04 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off'
2021-05-12 00:57:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 00:57:04 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:57:05 [DEBUG] Loading ..99%
2021-05-12 00:57:05 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 00:57:20 [DEBUG] 0% done
2021-05-12 00:57:20 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 00:57:20 [DEBUG] Cleaning
2021-05-12 00:57:20 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off"
2021-05-12 00:57:28 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:57:28 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:57:28 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:57:28 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off'
2021-05-12 00:57:28 [INFO ] Decoupling from GM
2021-05-12 00:57:28 [DEBUG] Decoupling FIXED_CSF1.OFF (outer surface) from FIXED_GM.OFF (inner surface)
2021-05-12 00:57:28 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_gm.off" --shells 2 --no-clean --intersect
2021-05-12 00:57:28 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:57:30 [DEBUG] Loading ..99%
2021-05-12 00:57:30 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 00:57:34 [DEBUG] Loading ..99%
2021-05-12 00:57:34 [DEBUG] INFO- Loaded 126022 vertices and 252044 faces.
2021-05-12 00:57:34 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_gm.off was joined.
2021-05-12 00:57:34 [DEBUG] 0% done
2021-05-12 00:57:34 [DEBUG] Testing for intersections ...
2021-05-12 00:57:53 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:57:53 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_gm.off" --shells 2 --no-clean --intersect
2021-05-12 00:57:53 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:57:55 [DEBUG] Loading ..99%
2021-05-12 00:57:55 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 00:57:59 [DEBUG] Loading ..99%
2021-05-12 00:57:59 [DEBUG] INFO- Loaded 126022 vertices and 252044 faces.
2021-05-12 00:57:59 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_gm.off was joined.
2021-05-12 00:57:59 [DEBUG] 0% done
2021-05-12 00:57:59 [DEBUG] Testing for intersections ...
2021-05-12 00:58:18 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:58:18 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by expanding FIXED_CSF1.OFF (outer surface)
2021-05-12 00:58:25 [DEBUG] Cleaning FIXED_CSF1.OFF (outer surface)
2021-05-12 00:58:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off"
2021-05-12 00:58:36 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:58:36 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:58:36 [DEBUG] Uniform remeshing ...
2021-05-12 00:58:36 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:58:36 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off'
2021-05-12 00:58:36 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off"
2021-05-12 00:58:45 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 00:58:45 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:58:45 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 00:58:45 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off'
2021-05-12 00:58:45 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_gm.off" --shells 2 --no-clean --intersect
2021-05-12 00:58:45 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 00:58:47 [DEBUG] Loading ..99%
2021-05-12 00:58:47 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 00:58:51 [DEBUG] Loading ..99%
2021-05-12 00:58:51 [DEBUG] INFO- Loaded 126022 vertices and 252044 faces.
2021-05-12 00:58:51 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_gm.off was joined.
2021-05-12 00:58:51 [DEBUG] 0% done
2021-05-12 00:58:51 [DEBUG] Testing for intersections ...
2021-05-12 00:59:10 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 00:59:10 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 00:59:10 [INFO ] Voxelizing
2021-05-12 00:59:10 [DEBUG] Creating csf.nii.gz from fixed_csf1.off
2021-05-12 00:59:12 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 01:00:50 [INFO ] CSF processing time: 00:07:13
2021-05-12 01:00:50 [INFO ] Processing VENTRICLES
2021-05-12 01:00:50 [INFO ] ========================================================================
2021-05-12 01:00:50 [INFO ] Fetching previously created files
2021-05-12 01:00:50 [INFO ] VENTRICLES processing time: 00:00:00
2021-05-12 01:00:50 [INFO ] Processing BONE
2021-05-12 01:00:50 [INFO ] ========================================================================
2021-05-12 01:00:50 [INFO ] Preparing volume for meshing
2021-05-12 01:00:52 [INFO ] Extracting surface
2021-05-12 01:00:52 [DEBUG] Generating surface mesh from mod_bone.nii.gz
2021-05-12 01:00:52 [DEBUG] Creating initial mesh
2021-05-12 01:00:58 [DEBUG] Keeping maximum 1 largest shell(s) with minimum area of 1
2021-05-12 01:00:58 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\mod_bone_mesh.off" -a 2.0 --no-clean -q --shells 1 --splitShells --shellMinArea 1 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone"
2021-05-12 01:01:13 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:01:13 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\mod_bone_mesh.off
2021-05-12 01:01:13 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:01:13 [DEBUG] Processing fixed_bone1.off
2021-05-12 01:01:13 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.stl"
2021-05-12 01:01:13 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:01:18 [DEBUG] Loading ..99%
2021-05-12 01:01:18 [DEBUG] INFO- Loaded 182702 vertices and 365780 faces.
2021-05-12 01:02:11 [DEBUG] 0% done
2021-05-12 01:02:11 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.stl'
2021-05-12 01:02:11 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 01:02:11 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off"
2021-05-12 01:03:39 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:03:39 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:03:39 [DEBUG] Uniform remeshing ...
2021-05-12 01:03:39 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:03:39 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off'
2021-05-12 01:03:39 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1_resampled.stl"
2021-05-12 01:03:39 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:03:42 [DEBUG] Loading ..99%
2021-05-12 01:03:42 [DEBUG] INFO- Loaded 76563 vertices and 153278 faces.
2021-05-12 01:04:04 [DEBUG] 0% done
2021-05-12 01:04:04 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1_resampled.stl'
2021-05-12 01:04:04 [DEBUG] Cleaning
2021-05-12 01:04:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off"
2021-05-12 01:04:19 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:04:19 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:04:19 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:04:19 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off'
2021-05-12 01:04:19 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1_resampled_clean.stl"
2021-05-12 01:04:20 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:04:22 [DEBUG] Loading ..99%
2021-05-12 01:04:22 [DEBUG] INFO- Loaded 76563 vertices and 153278 faces.
2021-05-12 01:04:44 [DEBUG] 0% done
2021-05-12 01:04:44 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1_resampled_clean.stl'
2021-05-12 01:04:44 [DEBUG] Smoothing 5 time(s)
2021-05-12 01:04:44 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off"
2021-05-12 01:04:45 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:04:45 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:04:47 [DEBUG] Loading ..99%
2021-05-12 01:04:47 [DEBUG] INFO- Loaded 76563 vertices and 153278 faces.
2021-05-12 01:04:47 [DEBUG] 0% done
2021-05-12 01:04:47 [DEBUG] Smoothing 5 steps.
2021-05-12 01:04:47 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 01:05:10 [DEBUG] 99 % done - 1 steps left
2021-05-12 01:05:10 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off'
2021-05-12 01:05:10 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1_resampled_clean_smoothed.stl"
2021-05-12 01:05:11 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:05:13 [DEBUG] Loading ..99%
2021-05-12 01:05:13 [DEBUG] INFO- Loaded 76563 vertices and 153278 faces.
2021-05-12 01:05:35 [DEBUG] 0% done
2021-05-12 01:05:35 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1_resampled_clean_smoothed.stl'
2021-05-12 01:05:35 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 01:05:35 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:05:36 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:05:36 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 01:05:36 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:05:38 [DEBUG] Loading ..99%
2021-05-12 01:05:38 [DEBUG] INFO- Loaded 76563 vertices and 153278 faces.
2021-05-12 01:05:40 [DEBUG] 0% done
2021-05-12 01:05:40 [DEBUG] Removing Spikes.
2021-05-12 01:05:40 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:05:40 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:05:40 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:05:52 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:05:52 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:05:55 [DEBUG] INFO- 20 intersecting triangles have been selected (in selection).
2021-05-12 01:05:58 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:06:06 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:06:06 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.667421 (38.240416 DEGs)
2021-05-12 01:06:06 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:06:06 [DEBUG] INFO- V: 76516
2021-05-12 01:06:06 [DEBUG] INFO- E: 229758
2021-05-12 01:06:06 [DEBUG] INFO- T: 153172
2021-05-12 01:06:06 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:06:06 [DEBUG] INFO- Handles: 36.
2021-05-12 01:06:06 [DEBUG] INFO- Shells: 1.
2021-05-12 01:06:06 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 01:06:06 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1_resampled_clean_smoothed_spike.stl"
2021-05-12 01:06:07 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:06:09 [DEBUG] Loading ..99%
2021-05-12 01:06:09 [DEBUG] INFO- Loaded 76563 vertices and 153278 faces.
2021-05-12 01:06:31 [DEBUG] 0% done
2021-05-12 01:06:31 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1_resampled_clean_smoothed_spike.stl'
2021-05-12 01:06:31 [DEBUG] Uniform remeshing
2021-05-12 01:06:31 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off"
2021-05-12 01:07:05 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:07:05 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:07:05 [DEBUG] Uniform remeshing ...
2021-05-12 01:07:05 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:07:05 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off'
2021-05-12 01:07:05 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 01:07:05 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:07:08 [DEBUG] Loading ..99%
2021-05-12 01:07:08 [DEBUG] INFO- Loaded 76555 vertices and 153254 faces.
2021-05-12 01:07:30 [DEBUG] 0% done
2021-05-12 01:07:30 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 01:07:30 [DEBUG] Cleaning
2021-05-12 01:07:30 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off"
2021-05-12 01:07:44 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:07:44 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:07:44 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:07:44 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off'
2021-05-12 01:07:44 [INFO ] Decoupling from CSF
2021-05-12 01:07:44 [DEBUG] Decoupling FIXED_BONE1.OFF (outer surface) from FIXED_CSF1.OFF (inner surface)
2021-05-12 01:07:44 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:07:44 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:07:46 [DEBUG] Loading ..99%
2021-05-12 01:07:46 [DEBUG] INFO- Loaded 76555 vertices and 153254 faces.
2021-05-12 01:07:48 [DEBUG] Loading ..99%
2021-05-12 01:07:48 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:07:48 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:07:48 [DEBUG] 0% done
2021-05-12 01:07:48 [DEBUG] Testing for intersections ...
2021-05-12 01:07:59 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:07:59 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:07:59 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:08:02 [DEBUG] Loading ..99%
2021-05-12 01:08:02 [DEBUG] INFO- Loaded 76555 vertices and 153254 faces.
2021-05-12 01:08:03 [DEBUG] Loading ..99%
2021-05-12 01:08:03 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:08:03 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:08:03 [DEBUG] 0% done
2021-05-12 01:08:03 [DEBUG] Testing for intersections ...
2021-05-12 01:08:14 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:08:14 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by expanding FIXED_BONE1.OFF (outer surface)
2021-05-12 01:08:22 [DEBUG] Moved 153.0 of 76555 vertices
2021-05-12 01:08:24 [DEBUG] Cleaning FIXED_BONE1.OFF (outer surface)
2021-05-12 01:08:24 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off"
2021-05-12 01:08:41 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:08:41 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:08:41 [DEBUG] Uniform remeshing ...
2021-05-12 01:08:41 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:08:41 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off'
2021-05-12 01:08:41 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off"
2021-05-12 01:08:55 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:08:55 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:08:55 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:08:55 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off'
2021-05-12 01:08:55 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:08:56 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:08:58 [DEBUG] Loading ..99%
2021-05-12 01:08:58 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:09:00 [DEBUG] Loading ..99%
2021-05-12 01:09:00 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:09:00 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:09:00 [DEBUG] 0% done
2021-05-12 01:09:00 [DEBUG] Testing for intersections ...
2021-05-12 01:09:11 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:09:11 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:09:11 [INFO ] Voxelizing
2021-05-12 01:09:11 [DEBUG] Creating bone.nii.gz from fixed_bone1.off
2021-05-12 01:09:13 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 01:12:10 [INFO ] Ensuring that the previously created surfaces are still decoupled
2021-05-12 01:12:10 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_gm.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:12:11 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_gm.off
2021-05-12 01:12:14 [DEBUG] Loading ..99%
2021-05-12 01:12:14 [DEBUG] INFO- Loaded 126022 vertices and 252044 faces.
2021-05-12 01:12:16 [DEBUG] Loading ..99%
2021-05-12 01:12:16 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:12:16 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:12:16 [DEBUG] 0% done
2021-05-12 01:12:16 [DEBUG] Testing for intersections ...
2021-05-12 01:12:36 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:12:36 [INFO ] BONE processing time: 00:11:46
2021-05-12 01:12:36 [INFO ] Processing SKIN
2021-05-12 01:12:36 [INFO ] ========================================================================
2021-05-12 01:12:36 [INFO ] Preparing volume for meshing
2021-05-12 01:12:37 [INFO ] Extracting surface
2021-05-12 01:12:37 [DEBUG] Generating surface mesh from mod_skin.nii.gz
2021-05-12 01:12:37 [DEBUG] Creating initial mesh
2021-05-12 01:12:44 [DEBUG] Keeping maximum 1 largest shell(s) with minimum area of 1
2021-05-12 01:12:44 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\mod_skin_mesh.off" -a 2.0 --no-clean -q --shells 1 --splitShells --shellMinArea 1 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin"
2021-05-12 01:13:02 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:13:02 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\mod_skin_mesh.off
2021-05-12 01:13:02 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:13:02 [DEBUG] Processing fixed_skin1.off
2021-05-12 01:13:02 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.stl"
2021-05-12 01:13:03 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:13:09 [DEBUG] Loading ..99%
2021-05-12 01:13:09 [DEBUG] INFO- Loaded 216156 vertices and 432400 faces.
2021-05-12 01:14:12 [DEBUG] 0% done
2021-05-12 01:14:12 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.stl'
2021-05-12 01:14:12 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 01:14:12 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off"
2021-05-12 01:15:54 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:15:54 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:15:54 [DEBUG] Uniform remeshing ...
2021-05-12 01:15:54 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:15:54 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off'
2021-05-12 01:15:54 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1_resampled.stl"
2021-05-12 01:15:54 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:15:57 [DEBUG] Loading ..99%
2021-05-12 01:15:57 [DEBUG] INFO- Loaded 92561 vertices and 185134 faces.
2021-05-12 01:16:24 [DEBUG] 0% done
2021-05-12 01:16:24 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1_resampled.stl'
2021-05-12 01:16:24 [DEBUG] Cleaning
2021-05-12 01:16:24 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off"
2021-05-12 01:16:41 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:16:41 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:16:41 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:16:41 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off'
2021-05-12 01:16:41 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1_resampled_clean.stl"
2021-05-12 01:16:41 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:16:44 [DEBUG] Loading ..99%
2021-05-12 01:16:44 [DEBUG] INFO- Loaded 92561 vertices and 185134 faces.
2021-05-12 01:17:11 [DEBUG] 0% done
2021-05-12 01:17:11 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1_resampled_clean.stl'
2021-05-12 01:17:11 [DEBUG] Smoothing 20 time(s)
2021-05-12 01:17:11 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" -a 2.0 --taubin 20 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off"
2021-05-12 01:17:12 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:17:12 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:17:14 [DEBUG] Loading ..99%
2021-05-12 01:17:14 [DEBUG] INFO- Loaded 92561 vertices and 185134 faces.
2021-05-12 01:17:15 [DEBUG] 0% done
2021-05-12 01:17:15 [DEBUG] Smoothing 20 steps.
2021-05-12 01:17:15 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 01:18:53 [DEBUG] 99 % done - 1 steps left
2021-05-12 01:18:53 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off'
2021-05-12 01:18:54 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1_resampled_clean_smoothed.stl"
2021-05-12 01:18:54 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:18:57 [DEBUG] Loading ..99%
2021-05-12 01:18:57 [DEBUG] INFO- Loaded 92561 vertices and 185134 faces.
2021-05-12 01:19:26 [DEBUG] 0% done
2021-05-12 01:19:26 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1_resampled_clean_smoothed.stl'
2021-05-12 01:19:26 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 01:19:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:19:26 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:19:26 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 01:19:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:19:29 [DEBUG] Loading ..99%
2021-05-12 01:19:29 [DEBUG] INFO- Loaded 92561 vertices and 185134 faces.
2021-05-12 01:19:31 [DEBUG] 0% done
2021-05-12 01:19:31 [DEBUG] Removing Spikes.
2021-05-12 01:19:31 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:19:31 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:19:31 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:19:37 [DEBUG] INFO- Removed the smallest 2 of 3 shells
2021-05-12 01:19:46 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:19:46 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:19:54 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:19:54 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.754061 (43.204495 DEGs)
2021-05-12 01:19:54 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:19:54 [DEBUG] INFO- V: 92488
2021-05-12 01:19:54 [DEBUG] INFO- E: 277470
2021-05-12 01:19:54 [DEBUG] INFO- T: 184980
2021-05-12 01:19:54 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:19:54 [DEBUG] INFO- Handles: 2.
2021-05-12 01:19:54 [DEBUG] INFO- Shells: 1.
2021-05-12 01:19:54 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 01:19:54 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1_resampled_clean_smoothed_spike.stl"
2021-05-12 01:19:54 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:19:57 [DEBUG] Loading ..99%
2021-05-12 01:19:57 [DEBUG] INFO- Loaded 92561 vertices and 185134 faces.
2021-05-12 01:20:25 [DEBUG] 0% done
2021-05-12 01:20:25 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1_resampled_clean_smoothed_spike.stl'
2021-05-12 01:20:25 [DEBUG] Uniform remeshing
2021-05-12 01:20:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off"
2021-05-12 01:21:05 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:21:05 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:21:05 [DEBUG] Uniform remeshing ...
2021-05-12 01:21:05 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:21:05 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off'
2021-05-12 01:21:05 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 01:21:05 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:21:08 [DEBUG] Loading ..99%
2021-05-12 01:21:08 [DEBUG] INFO- Loaded 92511 vertices and 185022 faces.
2021-05-12 01:21:35 [DEBUG] 0% done
2021-05-12 01:21:35 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 01:21:35 [DEBUG] Cleaning
2021-05-12 01:21:35 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off"
2021-05-12 01:21:51 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:21:51 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:21:51 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:21:51 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off'
2021-05-12 01:21:51 [INFO ] Decoupling from bone
2021-05-12 01:21:51 [DEBUG] Decoupling FIXED_SKIN1.OFF (outer surface) from FIXED_BONE1.OFF (inner surface)
2021-05-12 01:21:51 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:21:51 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:21:54 [DEBUG] Loading ..99%
2021-05-12 01:21:54 [DEBUG] INFO- Loaded 92511 vertices and 185022 faces.
2021-05-12 01:21:57 [DEBUG] Loading ..99%
2021-05-12 01:21:57 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:21:57 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:21:57 [DEBUG] 0% done
2021-05-12 01:21:57 [DEBUG] Testing for intersections ...
2021-05-12 01:22:04 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:22:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:22:04 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:22:07 [DEBUG] Loading ..99%
2021-05-12 01:22:07 [DEBUG] INFO- Loaded 92511 vertices and 185022 faces.
2021-05-12 01:22:10 [DEBUG] Loading ..99%
2021-05-12 01:22:10 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:22:10 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:22:10 [DEBUG] 0% done
2021-05-12 01:22:10 [DEBUG] Testing for intersections ...
2021-05-12 01:22:18 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:22:18 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by expanding FIXED_SKIN1.OFF (outer surface)
2021-05-12 01:22:27 [DEBUG] Moved 3.0 of 92511 vertices
2021-05-12 01:22:30 [DEBUG] Cleaning FIXED_SKIN1.OFF (outer surface)
2021-05-12 01:22:30 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off"
2021-05-12 01:22:51 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:22:51 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:22:51 [DEBUG] Uniform remeshing ...
2021-05-12 01:22:51 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:22:51 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off'
2021-05-12 01:22:51 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off"
2021-05-12 01:23:07 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:23:07 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:23:07 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:23:07 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off'
2021-05-12 01:23:07 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:23:07 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:23:10 [DEBUG] Loading ..99%
2021-05-12 01:23:10 [DEBUG] INFO- Loaded 92510 vertices and 185020 faces.
2021-05-12 01:23:13 [DEBUG] Loading ..99%
2021-05-12 01:23:13 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:23:13 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:23:13 [DEBUG] 0% done
2021-05-12 01:23:13 [DEBUG] Testing for intersections ...
2021-05-12 01:23:20 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:23:20 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:23:20 [INFO ] Voxelizing
2021-05-12 01:23:20 [DEBUG] Creating skin.nii.gz from fixed_skin1.off
2021-05-12 01:23:23 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 01:26:51 [INFO ] SKIN processing time: 00:14:15
2021-05-12 01:26:51 [INFO ] Processing EYES
2021-05-12 01:26:51 [INFO ] ========================================================================
2021-05-12 01:26:51 [INFO ] Extracting surfaces
2021-05-12 01:26:51 [DEBUG] Generating surface mesh from MASK_EYES.nii.gz
2021-05-12 01:26:51 [DEBUG] Creating initial mesh
2021-05-12 01:26:52 [DEBUG] Keeping maximum 2 largest shell(s) with minimum area of 1
2021-05-12 01:26:52 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\mask_prep\MASK_EYES_mesh.off" -a 2.0 --no-clean -q --shells 2 --splitShells --shellMinArea 1 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes"
2021-05-12 01:26:53 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:26:53 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\mask_prep\MASK_EYES_mesh.off
2021-05-12 01:26:53 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:53 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:26:53 [DEBUG] Processing fixed_eyes1.off
2021-05-12 01:26:53 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.stl"
2021-05-12 01:26:53 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:53 [DEBUG] Loading ..84%
2021-05-12 01:26:53 [DEBUG] INFO- Loaded 2370 vertices and 4740 faces.
2021-05-12 01:26:54 [DEBUG] 0% done
2021-05-12 01:26:54 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.stl'
2021-05-12 01:26:54 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 01:26:54 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off"
2021-05-12 01:26:54 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:26:54 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:54 [DEBUG] Uniform remeshing ...
2021-05-12 01:26:54 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:26:54 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off'
2021-05-12 01:26:54 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1_resampled.stl"
2021-05-12 01:26:54 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:54 [DEBUG] Loading ..96%
2021-05-12 01:26:54 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:26:55 [DEBUG] 0% done
2021-05-12 01:26:55 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1_resampled.stl'
2021-05-12 01:26:55 [DEBUG] Cleaning
2021-05-12 01:26:55 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off"
2021-05-12 01:26:55 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:26:55 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:55 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:26:55 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off'
2021-05-12 01:26:55 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1_resampled_clean.stl"
2021-05-12 01:26:55 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:55 [DEBUG] Loading ..96%
2021-05-12 01:26:55 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:26:56 [DEBUG] 0% done
2021-05-12 01:26:56 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1_resampled_clean.stl'
2021-05-12 01:26:56 [DEBUG] Smoothing 5 time(s)
2021-05-12 01:26:56 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off"
2021-05-12 01:26:56 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:26:56 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:56 [DEBUG] Loading ..96%
2021-05-12 01:26:56 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:26:56 [DEBUG] 0% done
2021-05-12 01:26:56 [DEBUG] Smoothing 5 steps.
2021-05-12 01:26:56 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 01:26:56 [DEBUG] 99 % done - 1 steps left
2021-05-12 01:26:56 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off'
2021-05-12 01:26:56 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1_resampled_clean_smoothed.stl"
2021-05-12 01:26:56 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:56 [DEBUG] Loading ..96%
2021-05-12 01:26:56 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:26:57 [DEBUG] 0% done
2021-05-12 01:26:57 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1_resampled_clean_smoothed.stl'
2021-05-12 01:26:57 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 01:26:57 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:57 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:26:57 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 01:26:57 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:57 [DEBUG] Loading ..96%
2021-05-12 01:26:57 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:26:57 [DEBUG] 0% done
2021-05-12 01:26:57 [DEBUG] Removing Spikes.
2021-05-12 01:26:57 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:26:57 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:26:57 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:26:57 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:26:57 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:26:57 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:26:57 [DEBUG] 100% done
2021-05-12 01:26:57 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 1.734994 (99.407828 DEGs)
2021-05-12 01:26:57 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:26:57 [DEBUG] INFO- V: 1032
2021-05-12 01:26:57 [DEBUG] INFO- E: 3090
2021-05-12 01:26:57 [DEBUG] INFO- T: 2060
2021-05-12 01:26:57 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:26:57 [DEBUG] INFO- Handles: 0.
2021-05-12 01:26:57 [DEBUG] INFO- Shells: 1.
2021-05-12 01:26:57 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 01:26:57 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1_resampled_clean_smoothed_spike.stl"
2021-05-12 01:26:57 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:57 [DEBUG] Loading ..96%
2021-05-12 01:26:57 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:26:57 [DEBUG] 0% done
2021-05-12 01:26:57 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1_resampled_clean_smoothed_spike.stl'
2021-05-12 01:26:57 [DEBUG] Uniform remeshing
2021-05-12 01:26:57 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off"
2021-05-12 01:26:58 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:26:58 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:58 [DEBUG] Uniform remeshing ...
2021-05-12 01:26:58 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:26:58 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off'
2021-05-12 01:26:58 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 01:26:58 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:58 [DEBUG] Loading ..96%
2021-05-12 01:26:58 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:26:58 [DEBUG] 0% done
2021-05-12 01:26:58 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 01:26:58 [DEBUG] Cleaning
2021-05-12 01:26:58 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off"
2021-05-12 01:26:58 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:26:58 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:26:58 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:26:58 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off'
2021-05-12 01:26:58 [DEBUG] Processing fixed_eyes2.off
2021-05-12 01:26:58 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.stl"
2021-05-12 01:26:59 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:26:59 [DEBUG] Loading ..89%
2021-05-12 01:26:59 [DEBUG] INFO- Loaded 2226 vertices and 4448 faces.
2021-05-12 01:26:59 [DEBUG] 0% done
2021-05-12 01:26:59 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.stl'
2021-05-12 01:26:59 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 01:26:59 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off"
2021-05-12 01:27:00 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:27:00 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:00 [DEBUG] Uniform remeshing ...
2021-05-12 01:27:00 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:27:00 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off'
2021-05-12 01:27:00 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2_resampled.stl"
2021-05-12 01:27:00 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:00 [DEBUG] Loading ..50%
2021-05-12 01:27:00 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:27:00 [DEBUG] 0% done
2021-05-12 01:27:00 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2_resampled.stl'
2021-05-12 01:27:00 [DEBUG] Cleaning
2021-05-12 01:27:00 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off"
2021-05-12 01:27:01 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:27:01 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:01 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:27:01 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off'
2021-05-12 01:27:01 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2_resampled_clean.stl"
2021-05-12 01:27:01 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:01 [DEBUG] Loading ..50%
2021-05-12 01:27:01 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:27:01 [DEBUG] 0% done
2021-05-12 01:27:01 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2_resampled_clean.stl'
2021-05-12 01:27:01 [DEBUG] Smoothing 5 time(s)
2021-05-12 01:27:01 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off"
2021-05-12 01:27:01 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:27:01 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:01 [DEBUG] Loading ..50%
2021-05-12 01:27:01 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:27:01 [DEBUG] 0% done
2021-05-12 01:27:01 [DEBUG] Smoothing 5 steps.
2021-05-12 01:27:01 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 01:27:01 [DEBUG] 80 % done - 1 steps left
2021-05-12 01:27:01 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off'
2021-05-12 01:27:02 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2_resampled_clean_smoothed.stl"
2021-05-12 01:27:02 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:02 [DEBUG] Loading ..50%
2021-05-12 01:27:02 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:27:02 [DEBUG] 0% done
2021-05-12 01:27:02 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2_resampled_clean_smoothed.stl'
2021-05-12 01:27:02 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 01:27:02 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:02 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:27:02 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 01:27:02 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:02 [DEBUG] Loading ..50%
2021-05-12 01:27:02 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:27:02 [DEBUG] 0% done
2021-05-12 01:27:02 [DEBUG] Removing Spikes.
2021-05-12 01:27:02 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:27:02 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:27:02 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:27:02 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:27:02 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:27:02 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:27:02 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 2.394374 (137.187522 DEGs)
2021-05-12 01:27:02 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:27:02 [DEBUG] INFO- V: 983
2021-05-12 01:27:02 [DEBUG] INFO- E: 2943
2021-05-12 01:27:02 [DEBUG] INFO- T: 1962
2021-05-12 01:27:02 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:27:02 [DEBUG] INFO- Handles: 0.
2021-05-12 01:27:02 [DEBUG] INFO- Shells: 1.
2021-05-12 01:27:02 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 01:27:02 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2_resampled_clean_smoothed_spike.stl"
2021-05-12 01:27:02 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:02 [DEBUG] Loading ..50%
2021-05-12 01:27:02 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:27:03 [DEBUG] 0% done
2021-05-12 01:27:03 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2_resampled_clean_smoothed_spike.stl'
2021-05-12 01:27:03 [DEBUG] Uniform remeshing
2021-05-12 01:27:03 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off"
2021-05-12 01:27:03 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:27:03 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:03 [DEBUG] Uniform remeshing ...
2021-05-12 01:27:03 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:27:03 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off'
2021-05-12 01:27:03 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 01:27:03 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:03 [DEBUG] Loading ..50%
2021-05-12 01:27:03 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:27:04 [DEBUG] 0% done
2021-05-12 01:27:04 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 01:27:04 [DEBUG] Cleaning
2021-05-12 01:27:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off"
2021-05-12 01:27:04 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:27:04 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:04 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:27:04 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off'
2021-05-12 01:27:04 [INFO ] Decoupling
2021-05-12 01:27:04 [INFO ] Decoupling fixed_eyes1 from bone
2021-05-12 01:27:04 [DEBUG] Decoupling FIXED_EYES1.OFF (surface 1) from FIXED_BONE1.OFF (surface 2)
2021-05-12 01:27:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:27:04 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:27:04 [DEBUG] Loading ..96%
2021-05-12 01:27:04 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:27:06 [DEBUG] Loading ..99%
2021-05-12 01:27:06 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:27:06 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:27:06 [DEBUG] 0% done
2021-05-12 01:27:06 [DEBUG] Testing for intersections ...
2021-05-12 01:27:10 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:27:10 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:27:10 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:27:10 [DEBUG] Loading ..96%
2021-05-12 01:27:10 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:27:12 [DEBUG] Loading ..99%
2021-05-12 01:27:12 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:27:12 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:27:12 [DEBUG] 0% done
2021-05-12 01:27:12 [DEBUG] Testing for intersections ...
2021-05-12 01:27:15 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:27:15 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_EYES1.OFF (surface 1)
2021-05-12 01:27:18 [DEBUG] Cleaning FIXED_EYES1.OFF (surface 1)
2021-05-12 01:27:18 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off"
2021-05-12 01:27:18 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:27:18 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:27:18 [DEBUG] Uniform remeshing ...
2021-05-12 01:27:18 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:27:18 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off'
2021-05-12 01:27:18 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off"
2021-05-12 01:27:18 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:27:18 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:27:18 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:27:18 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off'
2021-05-12 01:27:18 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:27:18 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:27:18 [DEBUG] Loading ..96%
2021-05-12 01:27:18 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:27:21 [DEBUG] Loading ..99%
2021-05-12 01:27:21 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:27:21 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:27:21 [DEBUG] 0% done
2021-05-12 01:27:21 [DEBUG] Testing for intersections ...
2021-05-12 01:27:24 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:27:24 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:27:24 [INFO ] Decoupling fixed_eyes1 from skin
2021-05-12 01:27:24 [DEBUG] Decoupling FIXED_EYES1.OFF (inner surface) from FIXED_SKIN1.OFF (outer surface)
2021-05-12 01:27:24 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --shells 2 --no-clean --intersect
2021-05-12 01:27:24 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:27:24 [DEBUG] Loading ..96%
2021-05-12 01:27:24 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:27:27 [DEBUG] Loading ..99%
2021-05-12 01:27:27 [DEBUG] INFO- Loaded 92510 vertices and 185020 faces.
2021-05-12 01:27:27 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off was joined.
2021-05-12 01:27:27 [DEBUG] 0% done
2021-05-12 01:27:27 [DEBUG] Testing for intersections ...
2021-05-12 01:27:29 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:27:29 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --shells 2 --no-clean --intersect
2021-05-12 01:27:29 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:27:29 [DEBUG] Loading ..96%
2021-05-12 01:27:29 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:27:32 [DEBUG] Loading ..99%
2021-05-12 01:27:32 [DEBUG] INFO- Loaded 92510 vertices and 185020 faces.
2021-05-12 01:27:32 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off was joined.
2021-05-12 01:27:32 [DEBUG] 0% done
2021-05-12 01:27:32 [DEBUG] Testing for intersections ...
2021-05-12 01:27:34 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:27:34 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_EYES1.OFF (inner surface)
2021-05-12 01:27:37 [DEBUG] Cleaning FIXED_EYES1.OFF (inner surface)
2021-05-12 01:27:37 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off"
2021-05-12 01:27:37 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:27:37 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:27:37 [DEBUG] Uniform remeshing ...
2021-05-12 01:27:37 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:27:37 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off'
2021-05-12 01:27:37 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off"
2021-05-12 01:27:37 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:27:37 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:27:37 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:27:37 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off'
2021-05-12 01:27:37 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --shells 2 --no-clean --intersect
2021-05-12 01:27:38 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:27:38 [DEBUG] Loading ..96%
2021-05-12 01:27:38 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:27:41 [DEBUG] Loading ..99%
2021-05-12 01:27:41 [DEBUG] INFO- Loaded 92510 vertices and 185020 faces.
2021-05-12 01:27:41 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off was joined.
2021-05-12 01:27:41 [DEBUG] 0% done
2021-05-12 01:27:41 [DEBUG] Testing for intersections ...
2021-05-12 01:27:43 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:27:43 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:27:43 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:27:43 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:27:43 [DEBUG] Loading ..96%
2021-05-12 01:27:43 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:27:45 [DEBUG] Loading ..99%
2021-05-12 01:27:45 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:27:45 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:27:45 [DEBUG] 0% done
2021-05-12 01:27:45 [DEBUG] Testing for intersections ...
2021-05-12 01:27:48 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:27:48 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --shells 2 --no-clean --intersect
2021-05-12 01:27:49 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:27:49 [DEBUG] Loading ..96%
2021-05-12 01:27:49 [DEBUG] INFO- Loaded 1033 vertices and 2062 faces.
2021-05-12 01:27:51 [DEBUG] Loading ..99%
2021-05-12 01:27:51 [DEBUG] INFO- Loaded 92510 vertices and 185020 faces.
2021-05-12 01:27:51 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off was joined.
2021-05-12 01:27:52 [DEBUG] 0% done
2021-05-12 01:27:52 [DEBUG] Testing for intersections ...
2021-05-12 01:27:53 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:27:53 [INFO ] Decoupling fixed_eyes2 from bone
2021-05-12 01:27:53 [DEBUG] Decoupling FIXED_EYES2.OFF (surface 1) from FIXED_BONE1.OFF (surface 2)
2021-05-12 01:27:53 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:27:54 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:54 [DEBUG] Loading ..50%
2021-05-12 01:27:54 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:27:56 [DEBUG] Loading ..99%
2021-05-12 01:27:56 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:27:56 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:27:56 [DEBUG] 0% done
2021-05-12 01:27:56 [DEBUG] Testing for intersections ...
2021-05-12 01:27:59 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:27:59 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:27:59 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:27:59 [DEBUG] Loading ..50%
2021-05-12 01:27:59 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:28:02 [DEBUG] Loading ..99%
2021-05-12 01:28:02 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:28:02 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:28:02 [DEBUG] 0% done
2021-05-12 01:28:02 [DEBUG] Testing for intersections ...
2021-05-12 01:28:05 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:28:05 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_EYES2.OFF (surface 1)
2021-05-12 01:28:07 [DEBUG] Cleaning FIXED_EYES2.OFF (surface 1)
2021-05-12 01:28:07 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off"
2021-05-12 01:28:07 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:28:07 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:28:07 [DEBUG] Uniform remeshing ...
2021-05-12 01:28:07 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:28:07 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off'
2021-05-12 01:28:07 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off"
2021-05-12 01:28:08 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:28:08 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:28:08 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:28:08 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off'
2021-05-12 01:28:08 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:28:08 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:28:08 [DEBUG] Loading ..50%
2021-05-12 01:28:08 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:28:10 [DEBUG] Loading ..99%
2021-05-12 01:28:10 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:28:10 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:28:10 [DEBUG] 0% done
2021-05-12 01:28:10 [DEBUG] Testing for intersections ...
2021-05-12 01:28:14 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:28:14 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:28:14 [INFO ] Decoupling fixed_eyes2 from skin
2021-05-12 01:28:14 [DEBUG] Decoupling FIXED_EYES2.OFF (inner surface) from FIXED_SKIN1.OFF (outer surface)
2021-05-12 01:28:14 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --shells 2 --no-clean --intersect
2021-05-12 01:28:14 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:28:14 [DEBUG] Loading ..50%
2021-05-12 01:28:14 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:28:17 [DEBUG] Loading ..99%
2021-05-12 01:28:17 [DEBUG] INFO- Loaded 92510 vertices and 185020 faces.
2021-05-12 01:28:17 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off was joined.
2021-05-12 01:28:17 [DEBUG] 0% done
2021-05-12 01:28:17 [DEBUG] Testing for intersections ...
2021-05-12 01:28:19 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:28:19 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --shells 2 --no-clean --intersect
2021-05-12 01:28:19 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:28:19 [DEBUG] Loading ..50%
2021-05-12 01:28:19 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:28:22 [DEBUG] Loading ..99%
2021-05-12 01:28:22 [DEBUG] INFO- Loaded 92510 vertices and 185020 faces.
2021-05-12 01:28:22 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off was joined.
2021-05-12 01:28:22 [DEBUG] 0% done
2021-05-12 01:28:22 [DEBUG] Testing for intersections ...
2021-05-12 01:28:24 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:28:24 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_EYES2.OFF (inner surface)
2021-05-12 01:28:27 [DEBUG] Cleaning FIXED_EYES2.OFF (inner surface)
2021-05-12 01:28:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off"
2021-05-12 01:28:27 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:28:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:28:27 [DEBUG] Uniform remeshing ...
2021-05-12 01:28:27 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:28:27 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off'
2021-05-12 01:28:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off"
2021-05-12 01:28:27 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:28:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:28:27 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:28:27 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off'
2021-05-12 01:28:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --shells 2 --no-clean --intersect
2021-05-12 01:28:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:28:27 [DEBUG] Loading ..50%
2021-05-12 01:28:27 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:28:30 [DEBUG] Loading ..99%
2021-05-12 01:28:30 [DEBUG] INFO- Loaded 92510 vertices and 185020 faces.
2021-05-12 01:28:30 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off was joined.
2021-05-12 01:28:30 [DEBUG] 0% done
2021-05-12 01:28:30 [DEBUG] Testing for intersections ...
2021-05-12 01:28:32 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:28:32 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:28:32 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:28:32 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:28:33 [DEBUG] Loading ..50%
2021-05-12 01:28:33 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:28:35 [DEBUG] Loading ..99%
2021-05-12 01:28:35 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:28:35 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:28:35 [DEBUG] 0% done
2021-05-12 01:28:35 [DEBUG] Testing for intersections ...
2021-05-12 01:28:38 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:28:38 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --shells 2 --no-clean --intersect
2021-05-12 01:28:38 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off
2021-05-12 01:28:38 [DEBUG] Loading ..50%
2021-05-12 01:28:38 [DEBUG] INFO- Loaded 983 vertices and 1962 faces.
2021-05-12 01:28:41 [DEBUG] Loading ..99%
2021-05-12 01:28:41 [DEBUG] INFO- Loaded 92510 vertices and 185020 faces.
2021-05-12 01:28:41 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off was joined.
2021-05-12 01:28:41 [DEBUG] 0% done
2021-05-12 01:28:41 [DEBUG] Testing for intersections ...
2021-05-12 01:28:43 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:28:43 [INFO ] Voxelizing
2021-05-12 01:28:43 [DEBUG] Creating eyes.nii.gz from fixed_eyes1.off
2021-05-12 01:28:43 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 01:28:50 [DEBUG] Creating eyes.nii.gz from fixed_eyes2.off
2021-05-12 01:28:50 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 01:28:56 [INFO ] EYES processing time: 00:02:05
2021-05-12 01:28:56 [INFO ] Processing INNER AIR CAVITIES
2021-05-12 01:28:56 [INFO ] ========================================================================
2021-05-12 01:28:56 [INFO ] Preparing volume for meshing
2021-05-12 01:28:58 [INFO ] Extracting surface(s)
2021-05-12 01:28:58 [DEBUG] Generating surface mesh from mod_cavities.nii.gz
2021-05-12 01:28:58 [DEBUG] Creating initial mesh
2021-05-12 01:28:59 [DEBUG] Keeping maximum 9 largest shell(s) with minimum area of 100
2021-05-12 01:28:59 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\mod_cavities_mesh.off" -a 2.0 --no-clean -q --shells 9 --splitShells --shellMinArea 100 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities"
2021-05-12 01:29:01 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:01 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\mod_cavities_mesh.off
2021-05-12 01:29:01 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:01 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:01 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:01 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:01 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:01 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:01 [DEBUG] Processing fixed_cavities1.off
2021-05-12 01:29:01 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.stl"
2021-05-12 01:29:01 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:01 [DEBUG] Loading ..98%
2021-05-12 01:29:01 [DEBUG] INFO- Loaded 4590 vertices and 9176 faces.
2021-05-12 01:29:02 [DEBUG] 0% done
2021-05-12 01:29:02 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.stl'
2021-05-12 01:29:02 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 01:29:02 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off"
2021-05-12 01:29:03 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:03 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:03 [DEBUG] Uniform remeshing ...
2021-05-12 01:29:03 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:03 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off'
2021-05-12 01:29:03 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1_resampled.stl"
2021-05-12 01:29:04 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:04 [DEBUG] Loading ..76%
2021-05-12 01:29:04 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:29:04 [DEBUG] 0% done
2021-05-12 01:29:04 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1_resampled.stl'
2021-05-12 01:29:04 [DEBUG] Cleaning
2021-05-12 01:29:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off"
2021-05-12 01:29:05 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:05 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:05 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:05 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off'
2021-05-12 01:29:05 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1_resampled_clean.stl"
2021-05-12 01:29:05 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:05 [DEBUG] Loading ..76%
2021-05-12 01:29:05 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:29:05 [DEBUG] 0% done
2021-05-12 01:29:05 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1_resampled_clean.stl'
2021-05-12 01:29:05 [DEBUG] Smoothing 5 time(s)
2021-05-12 01:29:05 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off"
2021-05-12 01:29:06 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:06 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:06 [DEBUG] Loading ..76%
2021-05-12 01:29:06 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:29:06 [DEBUG] 0% done
2021-05-12 01:29:06 [DEBUG] Smoothing 5 steps.
2021-05-12 01:29:06 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 01:29:06 [DEBUG] 90 % done - 1 steps left
2021-05-12 01:29:06 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off'
2021-05-12 01:29:06 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1_resampled_clean_smoothed.stl"
2021-05-12 01:29:06 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:06 [DEBUG] Loading ..76%
2021-05-12 01:29:06 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:29:07 [DEBUG] 0% done
2021-05-12 01:29:07 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1_resampled_clean_smoothed.stl'
2021-05-12 01:29:07 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 01:29:07 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:07 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:07 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 01:29:07 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:07 [DEBUG] Loading ..76%
2021-05-12 01:29:07 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:29:07 [DEBUG] 0% done
2021-05-12 01:29:07 [DEBUG] Removing Spikes.
2021-05-12 01:29:07 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:07 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:29:07 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:29:07 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:29:07 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:29:07 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:29:07 [DEBUG] 100% done
2021-05-12 01:29:07 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 1.503189 (86.126361 DEGs)
2021-05-12 01:29:07 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:29:07 [DEBUG] INFO- V: 1952
2021-05-12 01:29:07 [DEBUG] INFO- E: 5850
2021-05-12 01:29:07 [DEBUG] INFO- T: 3900
2021-05-12 01:29:07 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:29:07 [DEBUG] INFO- Handles: 0.
2021-05-12 01:29:07 [DEBUG] INFO- Shells: 1.
2021-05-12 01:29:07 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 01:29:07 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1_resampled_clean_smoothed_spike.stl"
2021-05-12 01:29:08 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:08 [DEBUG] Loading ..76%
2021-05-12 01:29:08 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:29:08 [DEBUG] 0% done
2021-05-12 01:29:08 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1_resampled_clean_smoothed_spike.stl'
2021-05-12 01:29:08 [DEBUG] Uniform remeshing
2021-05-12 01:29:08 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off"
2021-05-12 01:29:09 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:09 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:09 [DEBUG] Uniform remeshing ...
2021-05-12 01:29:09 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:09 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off'
2021-05-12 01:29:09 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 01:29:09 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:09 [DEBUG] Loading ..76%
2021-05-12 01:29:09 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:29:10 [DEBUG] 0% done
2021-05-12 01:29:10 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 01:29:10 [DEBUG] Cleaning
2021-05-12 01:29:10 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off"
2021-05-12 01:29:10 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:10 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:10 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:10 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off'
2021-05-12 01:29:10 [DEBUG] Processing fixed_cavities2.off
2021-05-12 01:29:10 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.stl"
2021-05-12 01:29:10 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:10 [DEBUG] Loading ..86%
2021-05-12 01:29:10 [DEBUG] INFO- Loaded 3452 vertices and 6900 faces.
2021-05-12 01:29:11 [DEBUG] 0% done
2021-05-12 01:29:11 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.stl'
2021-05-12 01:29:11 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 01:29:11 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off"
2021-05-12 01:29:12 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:12 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:12 [DEBUG] Uniform remeshing ...
2021-05-12 01:29:12 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:12 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off'
2021-05-12 01:29:12 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2_resampled.stl"
2021-05-12 01:29:12 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:12 [DEBUG] Loading ..66%
2021-05-12 01:29:12 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:29:13 [DEBUG] 0% done
2021-05-12 01:29:13 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2_resampled.stl'
2021-05-12 01:29:13 [DEBUG] Cleaning
2021-05-12 01:29:13 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off"
2021-05-12 01:29:13 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:13 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:13 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:13 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off'
2021-05-12 01:29:13 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2_resampled_clean.stl"
2021-05-12 01:29:13 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:13 [DEBUG] Loading ..66%
2021-05-12 01:29:13 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:29:14 [DEBUG] 0% done
2021-05-12 01:29:14 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2_resampled_clean.stl'
2021-05-12 01:29:14 [DEBUG] Smoothing 5 time(s)
2021-05-12 01:29:14 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off"
2021-05-12 01:29:14 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:14 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:14 [DEBUG] Loading ..66%
2021-05-12 01:29:14 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:29:14 [DEBUG] 0% done
2021-05-12 01:29:14 [DEBUG] Smoothing 5 steps.
2021-05-12 01:29:14 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 01:29:14 [DEBUG] 93 % done - 1 steps left
2021-05-12 01:29:14 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off'
2021-05-12 01:29:14 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2_resampled_clean_smoothed.stl"
2021-05-12 01:29:14 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:14 [DEBUG] Loading ..66%
2021-05-12 01:29:14 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:29:15 [DEBUG] 0% done
2021-05-12 01:29:15 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2_resampled_clean_smoothed.stl'
2021-05-12 01:29:15 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 01:29:15 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:15 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:15 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 01:29:15 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:15 [DEBUG] Loading ..66%
2021-05-12 01:29:15 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:29:15 [DEBUG] 0% done
2021-05-12 01:29:15 [DEBUG] Removing Spikes.
2021-05-12 01:29:15 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:15 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:29:15 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:29:15 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:29:15 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:29:15 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:29:15 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 1.596532 (91.474532 DEGs)
2021-05-12 01:29:15 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:29:15 [DEBUG] INFO- V: 1496
2021-05-12 01:29:15 [DEBUG] INFO- E: 4482
2021-05-12 01:29:15 [DEBUG] INFO- T: 2988
2021-05-12 01:29:15 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:29:15 [DEBUG] INFO- Handles: 0.
2021-05-12 01:29:15 [DEBUG] INFO- Shells: 1.
2021-05-12 01:29:15 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 01:29:15 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2_resampled_clean_smoothed_spike.stl"
2021-05-12 01:29:15 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:15 [DEBUG] Loading ..66%
2021-05-12 01:29:15 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:29:16 [DEBUG] 0% done
2021-05-12 01:29:16 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2_resampled_clean_smoothed_spike.stl'
2021-05-12 01:29:16 [DEBUG] Uniform remeshing
2021-05-12 01:29:16 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off"
2021-05-12 01:29:16 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:16 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:16 [DEBUG] Uniform remeshing ...
2021-05-12 01:29:16 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:16 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off'
2021-05-12 01:29:16 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 01:29:16 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:16 [DEBUG] Loading ..66%
2021-05-12 01:29:16 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:29:17 [DEBUG] 0% done
2021-05-12 01:29:17 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 01:29:17 [DEBUG] Cleaning
2021-05-12 01:29:17 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off"
2021-05-12 01:29:17 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:17 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:29:17 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:17 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off'
2021-05-12 01:29:17 [DEBUG] Processing fixed_cavities3.off
2021-05-12 01:29:17 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.stl"
2021-05-12 01:29:17 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:18 [DEBUG] Loading ..97%
2021-05-12 01:29:18 [DEBUG] INFO- Loaded 2560 vertices and 5128 faces.
2021-05-12 01:29:18 [DEBUG] 0% done
2021-05-12 01:29:18 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.stl'
2021-05-12 01:29:18 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 01:29:18 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off"
2021-05-12 01:29:19 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:19 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:19 [DEBUG] Uniform remeshing ...
2021-05-12 01:29:19 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:19 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off'
2021-05-12 01:29:19 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3_resampled.stl"
2021-05-12 01:29:19 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:19 [DEBUG] Loading ..91%
2021-05-12 01:29:19 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:29:20 [DEBUG] 0% done
2021-05-12 01:29:20 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3_resampled.stl'
2021-05-12 01:29:20 [DEBUG] Cleaning
2021-05-12 01:29:20 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off"
2021-05-12 01:29:20 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:20 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:20 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:20 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off'
2021-05-12 01:29:20 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3_resampled_clean.stl"
2021-05-12 01:29:20 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:20 [DEBUG] Loading ..91%
2021-05-12 01:29:20 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:29:21 [DEBUG] 0% done
2021-05-12 01:29:21 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3_resampled_clean.stl'
2021-05-12 01:29:21 [DEBUG] Smoothing 5 time(s)
2021-05-12 01:29:21 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off"
2021-05-12 01:29:21 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:21 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:21 [DEBUG] Loading ..91%
2021-05-12 01:29:21 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:29:21 [DEBUG] 0% done
2021-05-12 01:29:21 [DEBUG] Smoothing 5 steps.
2021-05-12 01:29:21 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 01:29:21 [DEBUG] 98 % done - 1 steps left
2021-05-12 01:29:21 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off'
2021-05-12 01:29:21 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3_resampled_clean_smoothed.stl"
2021-05-12 01:29:21 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:21 [DEBUG] Loading ..91%
2021-05-12 01:29:21 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:29:22 [DEBUG] 0% done
2021-05-12 01:29:22 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3_resampled_clean_smoothed.stl'
2021-05-12 01:29:22 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 01:29:22 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:22 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:22 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 01:29:22 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:22 [DEBUG] Loading ..91%
2021-05-12 01:29:22 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:29:22 [DEBUG] 0% done
2021-05-12 01:29:22 [DEBUG] Removing Spikes.
2021-05-12 01:29:22 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:22 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:29:22 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:29:22 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:29:22 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:29:22 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:29:22 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 1.521932 (87.200268 DEGs)
2021-05-12 01:29:22 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:29:22 [DEBUG] INFO- V: 1091
2021-05-12 01:29:22 [DEBUG] INFO- E: 3267
2021-05-12 01:29:22 [DEBUG] INFO- T: 2178
2021-05-12 01:29:22 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:29:22 [DEBUG] INFO- Handles: 0.
2021-05-12 01:29:22 [DEBUG] INFO- Shells: 1.
2021-05-12 01:29:22 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 01:29:22 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3_resampled_clean_smoothed_spike.stl"
2021-05-12 01:29:22 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:22 [DEBUG] Loading ..91%
2021-05-12 01:29:22 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:29:23 [DEBUG] 0% done
2021-05-12 01:29:23 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3_resampled_clean_smoothed_spike.stl'
2021-05-12 01:29:23 [DEBUG] Uniform remeshing
2021-05-12 01:29:23 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off"
2021-05-12 01:29:23 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:23 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:23 [DEBUG] Uniform remeshing ...
2021-05-12 01:29:23 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:23 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off'
2021-05-12 01:29:23 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 01:29:23 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:23 [DEBUG] Loading ..91%
2021-05-12 01:29:23 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:29:24 [DEBUG] 0% done
2021-05-12 01:29:24 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 01:29:24 [DEBUG] Cleaning
2021-05-12 01:29:24 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off"
2021-05-12 01:29:24 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:24 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:29:24 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:24 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off'
2021-05-12 01:29:24 [DEBUG] Processing fixed_cavities4.off
2021-05-12 01:29:24 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.stl"
2021-05-12 01:29:24 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:24 [DEBUG] Loading ..98%
2021-05-12 01:29:24 [DEBUG] INFO- Loaded 2030 vertices and 4064 faces.
2021-05-12 01:29:25 [DEBUG] 0% done
2021-05-12 01:29:25 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.stl'
2021-05-12 01:29:25 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 01:29:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off"
2021-05-12 01:29:25 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:25 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:25 [DEBUG] Uniform remeshing ...
2021-05-12 01:29:25 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:25 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off'
2021-05-12 01:29:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4_resampled.stl"
2021-05-12 01:29:25 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:25 [DEBUG] Loading ..55%
2021-05-12 01:29:25 [DEBUG] INFO- Loaded 896 vertices and 1792 faces.
2021-05-12 01:29:26 [DEBUG] 0% done
2021-05-12 01:29:26 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4_resampled.stl'
2021-05-12 01:29:26 [DEBUG] Cleaning
2021-05-12 01:29:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off"
2021-05-12 01:29:26 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:26 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:26 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off'
2021-05-12 01:29:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4_resampled_clean.stl"
2021-05-12 01:29:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:26 [DEBUG] Loading ..55%
2021-05-12 01:29:26 [DEBUG] INFO- Loaded 896 vertices and 1792 faces.
2021-05-12 01:29:26 [DEBUG] 0% done
2021-05-12 01:29:26 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4_resampled_clean.stl'
2021-05-12 01:29:26 [DEBUG] Smoothing 5 time(s)
2021-05-12 01:29:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off"
2021-05-12 01:29:27 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:27 [DEBUG] Loading ..55%
2021-05-12 01:29:27 [DEBUG] INFO- Loaded 896 vertices and 1792 faces.
2021-05-12 01:29:27 [DEBUG] 0% done
2021-05-12 01:29:27 [DEBUG] Smoothing 5 steps.
2021-05-12 01:29:27 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 01:29:27 [DEBUG] 80 % done - 1 steps left
2021-05-12 01:29:27 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off'
2021-05-12 01:29:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4_resampled_clean_smoothed.stl"
2021-05-12 01:29:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:27 [DEBUG] Loading ..55%
2021-05-12 01:29:27 [DEBUG] INFO- Loaded 896 vertices and 1792 faces.
2021-05-12 01:29:27 [DEBUG] 0% done
2021-05-12 01:29:27 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4_resampled_clean_smoothed.stl'
2021-05-12 01:29:27 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 01:29:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:27 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:27 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 01:29:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:27 [DEBUG] Loading ..55%
2021-05-12 01:29:27 [DEBUG] INFO- Loaded 896 vertices and 1792 faces.
2021-05-12 01:29:28 [DEBUG] 0% done
2021-05-12 01:29:28 [DEBUG] Removing Spikes.
2021-05-12 01:29:28 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:28 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:29:28 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:29:28 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:29:28 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:29:28 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:29:28 [DEBUG] 100% done
2021-05-12 01:29:28 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.641640 (36.763285 DEGs)
2021-05-12 01:29:28 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:29:28 [DEBUG] INFO- V: 882
2021-05-12 01:29:28 [DEBUG] INFO- E: 2646
2021-05-12 01:29:28 [DEBUG] INFO- T: 1764
2021-05-12 01:29:28 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:29:28 [DEBUG] INFO- Handles: 1.
2021-05-12 01:29:28 [DEBUG] INFO- Shells: 1.
2021-05-12 01:29:28 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 01:29:28 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4_resampled_clean_smoothed_spike.stl"
2021-05-12 01:29:28 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:28 [DEBUG] Loading ..55%
2021-05-12 01:29:28 [DEBUG] INFO- Loaded 896 vertices and 1792 faces.
2021-05-12 01:29:28 [DEBUG] 0% done
2021-05-12 01:29:28 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4_resampled_clean_smoothed_spike.stl'
2021-05-12 01:29:28 [DEBUG] Uniform remeshing
2021-05-12 01:29:28 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off"
2021-05-12 01:29:29 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:29 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:29 [DEBUG] Uniform remeshing ...
2021-05-12 01:29:29 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:29 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off'
2021-05-12 01:29:29 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 01:29:29 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:29 [DEBUG] Loading ..55%
2021-05-12 01:29:29 [DEBUG] INFO- Loaded 896 vertices and 1792 faces.
2021-05-12 01:29:29 [DEBUG] 0% done
2021-05-12 01:29:29 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 01:29:29 [DEBUG] Cleaning
2021-05-12 01:29:29 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off"
2021-05-12 01:29:30 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:30 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:29:30 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:30 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off'
2021-05-12 01:29:30 [DEBUG] Processing fixed_cavities5.off
2021-05-12 01:29:30 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.stl"
2021-05-12 01:29:30 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:30 [DEBUG] Loading ..99%
2021-05-12 01:29:30 [DEBUG] INFO- Loaded 1512 vertices and 3020 faces.
2021-05-12 01:29:30 [DEBUG] 0% done
2021-05-12 01:29:30 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.stl'
2021-05-12 01:29:30 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 01:29:30 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off"
2021-05-12 01:29:31 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:31 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:31 [DEBUG] Uniform remeshing ...
2021-05-12 01:29:31 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:31 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off'
2021-05-12 01:29:31 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5_resampled.stl"
2021-05-12 01:29:31 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:31 [DEBUG] Loading ..74%
2021-05-12 01:29:31 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:29:31 [DEBUG] 0% done
2021-05-12 01:29:31 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5_resampled.stl'
2021-05-12 01:29:31 [DEBUG] Cleaning
2021-05-12 01:29:31 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off"
2021-05-12 01:29:31 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:31 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:31 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:31 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off'
2021-05-12 01:29:31 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5_resampled_clean.stl"
2021-05-12 01:29:32 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:32 [DEBUG] Loading ..74%
2021-05-12 01:29:32 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:29:32 [DEBUG] 0% done
2021-05-12 01:29:32 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5_resampled_clean.stl'
2021-05-12 01:29:32 [DEBUG] Smoothing 5 time(s)
2021-05-12 01:29:32 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off"
2021-05-12 01:29:32 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:32 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:32 [DEBUG] Loading ..74%
2021-05-12 01:29:32 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:29:32 [DEBUG] 0% done
2021-05-12 01:29:32 [DEBUG] Smoothing 5 steps.
2021-05-12 01:29:32 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 01:29:32 [DEBUG] 80 % done - 1 steps left
2021-05-12 01:29:32 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off'
2021-05-12 01:29:32 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5_resampled_clean_smoothed.stl"
2021-05-12 01:29:32 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:32 [DEBUG] Loading ..74%
2021-05-12 01:29:32 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:29:32 [DEBUG] 0% done
2021-05-12 01:29:32 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5_resampled_clean_smoothed.stl'
2021-05-12 01:29:32 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 01:29:32 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:33 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:33 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 01:29:33 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:33 [DEBUG] Loading ..74%
2021-05-12 01:29:33 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:29:33 [DEBUG] 0% done
2021-05-12 01:29:33 [DEBUG] Removing Spikes.
2021-05-12 01:29:33 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:33 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:29:33 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:29:33 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:29:33 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:29:33 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:29:33 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 2.048018 (117.342806 DEGs)
2021-05-12 01:29:33 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:29:33 [DEBUG] INFO- V: 670
2021-05-12 01:29:33 [DEBUG] INFO- E: 2004
2021-05-12 01:29:33 [DEBUG] INFO- T: 1336
2021-05-12 01:29:33 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:29:33 [DEBUG] INFO- Handles: 0.
2021-05-12 01:29:33 [DEBUG] INFO- Shells: 1.
2021-05-12 01:29:33 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 01:29:33 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5_resampled_clean_smoothed_spike.stl"
2021-05-12 01:29:33 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:33 [DEBUG] Loading ..74%
2021-05-12 01:29:33 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:29:33 [DEBUG] 0% done
2021-05-12 01:29:33 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5_resampled_clean_smoothed_spike.stl'
2021-05-12 01:29:33 [DEBUG] Uniform remeshing
2021-05-12 01:29:33 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off"
2021-05-12 01:29:33 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:33 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:33 [DEBUG] Uniform remeshing ...
2021-05-12 01:29:33 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:33 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off'
2021-05-12 01:29:33 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 01:29:33 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:33 [DEBUG] Loading ..74%
2021-05-12 01:29:33 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:29:34 [DEBUG] 0% done
2021-05-12 01:29:34 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 01:29:34 [DEBUG] Cleaning
2021-05-12 01:29:34 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off"
2021-05-12 01:29:34 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:34 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:29:34 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:34 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off'
2021-05-12 01:29:34 [DEBUG] Processing fixed_cavities6.off
2021-05-12 01:29:34 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.stl"
2021-05-12 01:29:34 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:34 [DEBUG] Loading ..77%
2021-05-12 01:29:34 [DEBUG] INFO- Loaded 642 vertices and 1284 faces.
2021-05-12 01:29:34 [DEBUG] 0% done
2021-05-12 01:29:34 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.stl'
2021-05-12 01:29:34 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 01:29:34 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off"
2021-05-12 01:29:35 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:35 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:35 [DEBUG] Uniform remeshing ...
2021-05-12 01:29:35 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:35 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off'
2021-05-12 01:29:35 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6_resampled.stl"
2021-05-12 01:29:35 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:35 [DEBUG] Loading ..0%
2021-05-12 01:29:35 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:29:35 [DEBUG] 0% done
2021-05-12 01:29:35 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6_resampled.stl'
2021-05-12 01:29:35 [DEBUG] Cleaning
2021-05-12 01:29:35 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off"
2021-05-12 01:29:35 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:35 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:35 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:35 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off'
2021-05-12 01:29:35 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6_resampled_clean.stl"
2021-05-12 01:29:35 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:35 [DEBUG] Loading ..0%
2021-05-12 01:29:35 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:29:35 [DEBUG] 0% done
2021-05-12 01:29:35 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6_resampled_clean.stl'
2021-05-12 01:29:35 [DEBUG] Smoothing 5 time(s)
2021-05-12 01:29:35 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off"
2021-05-12 01:29:35 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:35 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:35 [DEBUG] Loading ..0%
2021-05-12 01:29:35 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:29:35 [DEBUG] 0% done
2021-05-12 01:29:35 [DEBUG] Smoothing 5 steps.
2021-05-12 01:29:35 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 01:29:35 [DEBUG] 80 % done - 1 steps left
2021-05-12 01:29:35 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off'
2021-05-12 01:29:35 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6_resampled_clean_smoothed.stl"
2021-05-12 01:29:36 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:36 [DEBUG] Loading ..0%
2021-05-12 01:29:36 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:29:36 [DEBUG] 0% done
2021-05-12 01:29:36 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6_resampled_clean_smoothed.stl'
2021-05-12 01:29:36 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 01:29:36 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:36 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:36 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 01:29:36 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:36 [DEBUG] Loading ..0%
2021-05-12 01:29:36 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:29:36 [DEBUG] 0% done
2021-05-12 01:29:36 [DEBUG] Removing Spikes.
2021-05-12 01:29:36 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:36 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:29:36 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:29:36 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:29:36 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:29:36 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:29:36 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 0.299145 (17.139747 DEGs)
2021-05-12 01:29:36 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:29:36 [DEBUG] INFO- V: 305
2021-05-12 01:29:36 [DEBUG] INFO- E: 915
2021-05-12 01:29:36 [DEBUG] INFO- T: 610
2021-05-12 01:29:36 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:29:36 [DEBUG] INFO- Handles: 1.
2021-05-12 01:29:36 [DEBUG] INFO- Shells: 1.
2021-05-12 01:29:36 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 01:29:36 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6_resampled_clean_smoothed_spike.stl"
2021-05-12 01:29:36 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:36 [DEBUG] Loading ..0%
2021-05-12 01:29:36 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:29:36 [DEBUG] 0% done
2021-05-12 01:29:36 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6_resampled_clean_smoothed_spike.stl'
2021-05-12 01:29:36 [DEBUG] Uniform remeshing
2021-05-12 01:29:36 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off"
2021-05-12 01:29:36 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:36 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:36 [DEBUG] Uniform remeshing ...
2021-05-12 01:29:36 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:36 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off'
2021-05-12 01:29:36 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 01:29:37 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:37 [DEBUG] Loading ..0%
2021-05-12 01:29:37 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:29:37 [DEBUG] 0% done
2021-05-12 01:29:37 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 01:29:37 [DEBUG] Cleaning
2021-05-12 01:29:37 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off"
2021-05-12 01:29:37 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:37 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:29:37 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:37 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off'
2021-05-12 01:29:37 [INFO ] Decoupling
2021-05-12 01:29:37 [INFO ] Decoupling fixed_cavities1 from CSF
2021-05-12 01:29:37 [DEBUG] Decoupling FIXED_CAVITIES1.OFF (surface 1) from FIXED_CSF1.OFF (surface 2)
2021-05-12 01:29:37 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:29:37 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:37 [DEBUG] Loading ..76%
2021-05-12 01:29:37 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:29:38 [DEBUG] Loading ..99%
2021-05-12 01:29:38 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:29:38 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:29:39 [DEBUG] 0% done
2021-05-12 01:29:39 [DEBUG] Testing for intersections ...
2021-05-12 01:29:40 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:29:40 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:29:40 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:40 [DEBUG] Loading ..76%
2021-05-12 01:29:40 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:29:41 [DEBUG] Loading ..99%
2021-05-12 01:29:41 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:29:41 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:29:41 [DEBUG] 0% done
2021-05-12 01:29:41 [DEBUG] Testing for intersections ...
2021-05-12 01:29:42 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:29:42 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_CAVITIES1.OFF (surface 1)
2021-05-12 01:29:44 [DEBUG] Cleaning FIXED_CAVITIES1.OFF (surface 1)
2021-05-12 01:29:44 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off"
2021-05-12 01:29:44 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:44 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:44 [DEBUG] Uniform remeshing ...
2021-05-12 01:29:44 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:44 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off'
2021-05-12 01:29:44 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off"
2021-05-12 01:29:45 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:29:45 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:45 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:29:45 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off'
2021-05-12 01:29:45 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:29:45 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:45 [DEBUG] Loading ..76%
2021-05-12 01:29:45 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:29:47 [DEBUG] Loading ..99%
2021-05-12 01:29:47 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:29:47 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:29:47 [DEBUG] 0% done
2021-05-12 01:29:47 [DEBUG] Testing for intersections ...
2021-05-12 01:29:48 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:29:48 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:29:48 [INFO ] Decoupling fixed_cavities1 from bone
2021-05-12 01:29:48 [DEBUG] Decoupling FIXED_CAVITIES1.OFF (inner surface) from FIXED_BONE1.OFF (outer surface)
2021-05-12 01:29:48 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:29:48 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:48 [DEBUG] Loading ..76%
2021-05-12 01:29:48 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:29:50 [DEBUG] Loading ..99%
2021-05-12 01:29:50 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:29:50 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:29:50 [DEBUG] 0% done
2021-05-12 01:29:50 [DEBUG] Testing for intersections ...
2021-05-12 01:29:54 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:29:54 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:29:54 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:29:54 [DEBUG] Loading ..76%
2021-05-12 01:29:54 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:29:56 [DEBUG] Loading ..99%
2021-05-12 01:29:56 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:29:56 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:29:56 [DEBUG] 0% done
2021-05-12 01:29:56 [DEBUG] Testing for intersections ...
2021-05-12 01:30:00 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:30:00 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_CAVITIES1.OFF (inner surface)
2021-05-12 01:30:02 [DEBUG] Cleaning FIXED_CAVITIES1.OFF (inner surface)
2021-05-12 01:30:02 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off"
2021-05-12 01:30:02 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:30:02 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:30:02 [DEBUG] Uniform remeshing ...
2021-05-12 01:30:02 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:30:02 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off'
2021-05-12 01:30:02 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off"
2021-05-12 01:30:03 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:30:03 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:30:03 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:30:03 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off'
2021-05-12 01:30:03 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:30:03 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:30:03 [DEBUG] Loading ..76%
2021-05-12 01:30:03 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:30:05 [DEBUG] Loading ..99%
2021-05-12 01:30:05 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:30:05 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:30:05 [DEBUG] 0% done
2021-05-12 01:30:05 [DEBUG] Testing for intersections ...
2021-05-12 01:30:09 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:30:09 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:30:09 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:30:09 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:30:09 [DEBUG] Loading ..76%
2021-05-12 01:30:09 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:30:10 [DEBUG] Loading ..99%
2021-05-12 01:30:10 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:30:10 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:30:10 [DEBUG] 0% done
2021-05-12 01:30:10 [DEBUG] Testing for intersections ...
2021-05-12 01:30:12 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:30:12 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:30:12 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:30:12 [DEBUG] Loading ..76%
2021-05-12 01:30:12 [DEBUG] INFO- Loaded 1957 vertices and 3910 faces.
2021-05-12 01:30:14 [DEBUG] Loading ..99%
2021-05-12 01:30:14 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:30:14 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:30:14 [DEBUG] 0% done
2021-05-12 01:30:14 [DEBUG] Testing for intersections ...
2021-05-12 01:30:17 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:30:17 [INFO ] Decoupling fixed_cavities2 from CSF
2021-05-12 01:30:17 [DEBUG] Decoupling FIXED_CAVITIES2.OFF (surface 1) from FIXED_CSF1.OFF (surface 2)
2021-05-12 01:30:17 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:30:18 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:30:18 [DEBUG] Loading ..66%
2021-05-12 01:30:18 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:30:19 [DEBUG] Loading ..99%
2021-05-12 01:30:19 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:30:19 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:30:19 [DEBUG] 0% done
2021-05-12 01:30:19 [DEBUG] Testing for intersections ...
2021-05-12 01:30:21 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:30:21 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:30:21 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:30:21 [DEBUG] Loading ..66%
2021-05-12 01:30:21 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:30:22 [DEBUG] Loading ..99%
2021-05-12 01:30:22 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:30:22 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:30:22 [DEBUG] 0% done
2021-05-12 01:30:22 [DEBUG] Testing for intersections ...
2021-05-12 01:30:23 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:30:23 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_CAVITIES2.OFF (surface 1)
2021-05-12 01:30:25 [DEBUG] Moved 133.0 of 1496 vertices
2021-05-12 01:30:25 [DEBUG] Cleaning FIXED_CAVITIES2.OFF (surface 1)
2021-05-12 01:30:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off"
2021-05-12 01:30:25 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:30:25 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:30:25 [DEBUG] Uniform remeshing ...
2021-05-12 01:30:25 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:30:25 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off'
2021-05-12 01:30:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off"
2021-05-12 01:30:26 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:30:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:30:26 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:30:26 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off'
2021-05-12 01:30:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:30:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:30:26 [DEBUG] Loading ..66%
2021-05-12 01:30:26 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:30:27 [DEBUG] Loading ..99%
2021-05-12 01:30:27 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:30:27 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:30:28 [DEBUG] 0% done
2021-05-12 01:30:28 [DEBUG] Testing for intersections ...
2021-05-12 01:30:29 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:30:29 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:30:29 [INFO ] Decoupling fixed_cavities2 from bone
2021-05-12 01:30:29 [DEBUG] Decoupling FIXED_CAVITIES2.OFF (inner surface) from FIXED_BONE1.OFF (outer surface)
2021-05-12 01:30:29 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:30:29 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:30:29 [DEBUG] Loading ..66%
2021-05-12 01:30:29 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:30:31 [DEBUG] Loading ..99%
2021-05-12 01:30:31 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:30:31 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:30:31 [DEBUG] 0% done
2021-05-12 01:30:31 [DEBUG] Testing for intersections ...
2021-05-12 01:30:35 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:30:35 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:30:35 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:30:35 [DEBUG] Loading ..66%
2021-05-12 01:30:35 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:30:37 [DEBUG] Loading ..99%
2021-05-12 01:30:37 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:30:37 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:30:37 [DEBUG] 0% done
2021-05-12 01:30:37 [DEBUG] Testing for intersections ...
2021-05-12 01:30:41 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:30:41 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_CAVITIES2.OFF (inner surface)
2021-05-12 01:30:43 [DEBUG] Cleaning FIXED_CAVITIES2.OFF (inner surface)
2021-05-12 01:30:43 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off"
2021-05-12 01:30:43 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:30:43 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:30:43 [DEBUG] Uniform remeshing ...
2021-05-12 01:30:43 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:30:43 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off'
2021-05-12 01:30:43 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off"
2021-05-12 01:30:44 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:30:44 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:30:44 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:30:44 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off'
2021-05-12 01:30:44 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:30:44 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:30:44 [DEBUG] Loading ..66%
2021-05-12 01:30:44 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:30:46 [DEBUG] Loading ..99%
2021-05-12 01:30:46 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:30:46 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:30:46 [DEBUG] 0% done
2021-05-12 01:30:46 [DEBUG] Testing for intersections ...
2021-05-12 01:30:49 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:30:49 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:30:49 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:30:50 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:30:50 [DEBUG] Loading ..66%
2021-05-12 01:30:50 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:30:51 [DEBUG] Loading ..99%
2021-05-12 01:30:51 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:30:51 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:30:51 [DEBUG] 0% done
2021-05-12 01:30:51 [DEBUG] Testing for intersections ...
2021-05-12 01:30:52 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:30:52 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:30:53 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off
2021-05-12 01:30:53 [DEBUG] Loading ..66%
2021-05-12 01:30:53 [DEBUG] INFO- Loaded 1496 vertices and 2988 faces.
2021-05-12 01:30:55 [DEBUG] Loading ..99%
2021-05-12 01:30:55 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:30:55 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:30:55 [DEBUG] 0% done
2021-05-12 01:30:55 [DEBUG] Testing for intersections ...
2021-05-12 01:30:58 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:30:58 [INFO ] Decoupling fixed_cavities3 from CSF
2021-05-12 01:30:58 [DEBUG] Decoupling FIXED_CAVITIES3.OFF (surface 1) from FIXED_CSF1.OFF (surface 2)
2021-05-12 01:30:58 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:30:58 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:30:59 [DEBUG] Loading ..91%
2021-05-12 01:30:59 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:31:00 [DEBUG] Loading ..99%
2021-05-12 01:31:00 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:31:00 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:31:00 [DEBUG] 0% done
2021-05-12 01:31:00 [DEBUG] Testing for intersections ...
2021-05-12 01:31:01 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:31:01 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:31:01 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:31:01 [DEBUG] Loading ..91%
2021-05-12 01:31:01 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:31:03 [DEBUG] Loading ..99%
2021-05-12 01:31:03 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:31:03 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:31:03 [DEBUG] 0% done
2021-05-12 01:31:03 [DEBUG] Testing for intersections ...
2021-05-12 01:31:04 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:31:04 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_CAVITIES3.OFF (surface 1)
2021-05-12 01:31:06 [DEBUG] Moved 51.0 of 1092 vertices
2021-05-12 01:31:06 [DEBUG] Cleaning FIXED_CAVITIES3.OFF (surface 1)
2021-05-12 01:31:06 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off"
2021-05-12 01:31:06 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:31:06 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:31:06 [DEBUG] Uniform remeshing ...
2021-05-12 01:31:06 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:31:06 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off'
2021-05-12 01:31:06 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off"
2021-05-12 01:31:06 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:31:06 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:31:06 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:31:06 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off'
2021-05-12 01:31:06 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:31:06 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:31:06 [DEBUG] Loading ..91%
2021-05-12 01:31:06 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:31:08 [DEBUG] Loading ..99%
2021-05-12 01:31:08 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:31:08 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:31:08 [DEBUG] 0% done
2021-05-12 01:31:08 [DEBUG] Testing for intersections ...
2021-05-12 01:31:09 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:31:09 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:31:09 [INFO ] Decoupling fixed_cavities3 from bone
2021-05-12 01:31:09 [DEBUG] Decoupling FIXED_CAVITIES3.OFF (inner surface) from FIXED_BONE1.OFF (outer surface)
2021-05-12 01:31:09 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:31:09 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:31:09 [DEBUG] Loading ..91%
2021-05-12 01:31:09 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:31:12 [DEBUG] Loading ..99%
2021-05-12 01:31:12 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:31:12 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:31:12 [DEBUG] 0% done
2021-05-12 01:31:12 [DEBUG] Testing for intersections ...
2021-05-12 01:31:15 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:31:15 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:31:15 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:31:15 [DEBUG] Loading ..91%
2021-05-12 01:31:15 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:31:18 [DEBUG] Loading ..99%
2021-05-12 01:31:18 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:31:18 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:31:18 [DEBUG] 0% done
2021-05-12 01:31:18 [DEBUG] Testing for intersections ...
2021-05-12 01:31:22 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:31:22 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_CAVITIES3.OFF (inner surface)
2021-05-12 01:31:24 [DEBUG] Cleaning FIXED_CAVITIES3.OFF (inner surface)
2021-05-12 01:31:24 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off"
2021-05-12 01:31:24 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:31:24 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:31:24 [DEBUG] Uniform remeshing ...
2021-05-12 01:31:24 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:31:24 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off'
2021-05-12 01:31:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off"
2021-05-12 01:31:25 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:31:25 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:31:25 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:31:25 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off'
2021-05-12 01:31:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:31:25 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:31:25 [DEBUG] Loading ..91%
2021-05-12 01:31:25 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:31:27 [DEBUG] Loading ..99%
2021-05-12 01:31:27 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:31:27 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:31:27 [DEBUG] 0% done
2021-05-12 01:31:27 [DEBUG] Testing for intersections ...
2021-05-12 01:31:31 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:31:31 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:31:31 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:31:31 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:31:31 [DEBUG] Loading ..91%
2021-05-12 01:31:31 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:31:32 [DEBUG] Loading ..99%
2021-05-12 01:31:32 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:31:32 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:31:32 [DEBUG] 0% done
2021-05-12 01:31:32 [DEBUG] Testing for intersections ...
2021-05-12 01:31:34 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:31:34 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:31:34 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off
2021-05-12 01:31:34 [DEBUG] Loading ..91%
2021-05-12 01:31:34 [DEBUG] INFO- Loaded 1092 vertices and 2180 faces.
2021-05-12 01:31:36 [DEBUG] Loading ..99%
2021-05-12 01:31:36 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:31:36 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:31:36 [DEBUG] 0% done
2021-05-12 01:31:36 [DEBUG] Testing for intersections ...
2021-05-12 01:31:39 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:31:39 [INFO ] Decoupling fixed_cavities4 from CSF
2021-05-12 01:31:39 [DEBUG] Decoupling FIXED_CAVITIES4.OFF (surface 1) from FIXED_CSF1.OFF (surface 2)
2021-05-12 01:31:39 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:31:39 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:31:40 [DEBUG] Loading ..55%
2021-05-12 01:31:40 [DEBUG] INFO- Loaded 896 vertices and 1792 faces.
2021-05-12 01:31:41 [DEBUG] Loading ..99%
2021-05-12 01:31:41 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:31:41 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:31:41 [DEBUG] 0% done
2021-05-12 01:31:41 [DEBUG] Testing for intersections ...
2021-05-12 01:31:42 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:31:42 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:31:42 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:31:42 [DEBUG] Loading ..55%
2021-05-12 01:31:42 [DEBUG] INFO- Loaded 896 vertices and 1792 faces.
2021-05-12 01:31:44 [DEBUG] Loading ..99%
2021-05-12 01:31:44 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:31:44 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:31:44 [DEBUG] 0% done
2021-05-12 01:31:44 [DEBUG] Testing for intersections ...
2021-05-12 01:31:45 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:31:45 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_CAVITIES4.OFF (surface 1)
2021-05-12 01:31:46 [DEBUG] Cleaning FIXED_CAVITIES4.OFF (surface 1)
2021-05-12 01:31:46 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off"
2021-05-12 01:31:47 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:31:47 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:31:47 [DEBUG] Uniform remeshing ...
2021-05-12 01:31:47 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:31:47 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off'
2021-05-12 01:31:47 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off"
2021-05-12 01:31:47 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:31:47 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:31:47 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:31:47 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off'
2021-05-12 01:31:47 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:31:47 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:31:47 [DEBUG] Loading ..55%
2021-05-12 01:31:47 [DEBUG] INFO- Loaded 896 vertices and 1792 faces.
2021-05-12 01:31:49 [DEBUG] Loading ..99%
2021-05-12 01:31:49 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:31:49 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:31:49 [DEBUG] 0% done
2021-05-12 01:31:49 [DEBUG] Testing for intersections ...
2021-05-12 01:31:50 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:31:50 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:31:50 [INFO ] Decoupling fixed_cavities4 from bone
2021-05-12 01:31:50 [DEBUG] Decoupling FIXED_CAVITIES4.OFF (inner surface) from FIXED_BONE1.OFF (outer surface)
2021-05-12 01:31:50 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:31:50 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:31:50 [DEBUG] Loading ..55%
2021-05-12 01:31:50 [DEBUG] INFO- Loaded 896 vertices and 1792 faces.
2021-05-12 01:31:52 [DEBUG] Loading ..99%
2021-05-12 01:31:52 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:31:52 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:31:52 [DEBUG] 0% done
2021-05-12 01:31:52 [DEBUG] Testing for intersections ...
2021-05-12 01:31:55 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:31:55 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:31:56 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:31:56 [DEBUG] Loading ..55%
2021-05-12 01:31:56 [DEBUG] INFO- Loaded 896 vertices and 1792 faces.
2021-05-12 01:31:58 [DEBUG] Loading ..99%
2021-05-12 01:31:58 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:31:58 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:31:58 [DEBUG] 0% done
2021-05-12 01:31:58 [DEBUG] Testing for intersections ...
2021-05-12 01:32:01 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:32:01 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_CAVITIES4.OFF (inner surface)
2021-05-12 01:32:04 [DEBUG] Cleaning FIXED_CAVITIES4.OFF (inner surface)
2021-05-12 01:32:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off"
2021-05-12 01:32:04 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:32:04 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:32:04 [DEBUG] Uniform remeshing ...
2021-05-12 01:32:04 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:32:04 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off'
2021-05-12 01:32:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off"
2021-05-12 01:32:04 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:32:04 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:32:04 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:32:04 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off'
2021-05-12 01:32:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:32:04 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:32:05 [DEBUG] Loading ..56%
2021-05-12 01:32:05 [DEBUG] INFO- Loaded 892 vertices and 1780 faces.
2021-05-12 01:32:07 [DEBUG] Loading ..99%
2021-05-12 01:32:07 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:32:07 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:32:07 [DEBUG] 0% done
2021-05-12 01:32:07 [DEBUG] Testing for intersections ...
2021-05-12 01:32:10 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:32:10 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:32:10 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:32:10 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:32:10 [DEBUG] Loading ..56%
2021-05-12 01:32:10 [DEBUG] INFO- Loaded 892 vertices and 1780 faces.
2021-05-12 01:32:12 [DEBUG] Loading ..99%
2021-05-12 01:32:12 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:32:12 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:32:12 [DEBUG] 0% done
2021-05-12 01:32:12 [DEBUG] Testing for intersections ...
2021-05-12 01:32:13 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:32:13 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:32:13 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off
2021-05-12 01:32:13 [DEBUG] Loading ..56%
2021-05-12 01:32:13 [DEBUG] INFO- Loaded 892 vertices and 1780 faces.
2021-05-12 01:32:15 [DEBUG] Loading ..99%
2021-05-12 01:32:15 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:32:15 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:32:15 [DEBUG] 0% done
2021-05-12 01:32:15 [DEBUG] Testing for intersections ...
2021-05-12 01:32:19 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:32:19 [INFO ] Decoupling fixed_cavities5 from CSF
2021-05-12 01:32:19 [DEBUG] Decoupling FIXED_CAVITIES5.OFF (surface 1) from FIXED_CSF1.OFF (surface 2)
2021-05-12 01:32:19 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:32:19 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:32:19 [DEBUG] Loading ..74%
2021-05-12 01:32:19 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:32:20 [DEBUG] Loading ..99%
2021-05-12 01:32:20 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:32:20 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:32:20 [DEBUG] 0% done
2021-05-12 01:32:20 [DEBUG] Testing for intersections ...
2021-05-12 01:32:21 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:32:22 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:32:22 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:32:22 [DEBUG] Loading ..74%
2021-05-12 01:32:22 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:32:23 [DEBUG] Loading ..99%
2021-05-12 01:32:23 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:32:23 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:32:23 [DEBUG] 0% done
2021-05-12 01:32:23 [DEBUG] Testing for intersections ...
2021-05-12 01:32:24 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:32:24 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_CAVITIES5.OFF (surface 1)
2021-05-12 01:32:26 [DEBUG] Cleaning FIXED_CAVITIES5.OFF (surface 1)
2021-05-12 01:32:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off"
2021-05-12 01:32:26 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:32:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:32:26 [DEBUG] Uniform remeshing ...
2021-05-12 01:32:26 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:32:26 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off'
2021-05-12 01:32:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off"
2021-05-12 01:32:26 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:32:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:32:26 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:32:26 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off'
2021-05-12 01:32:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:32:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:32:26 [DEBUG] Loading ..74%
2021-05-12 01:32:26 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:32:28 [DEBUG] Loading ..99%
2021-05-12 01:32:28 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:32:28 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:32:28 [DEBUG] 0% done
2021-05-12 01:32:28 [DEBUG] Testing for intersections ...
2021-05-12 01:32:29 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:32:29 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:32:29 [INFO ] Decoupling fixed_cavities5 from bone
2021-05-12 01:32:29 [DEBUG] Decoupling FIXED_CAVITIES5.OFF (inner surface) from FIXED_BONE1.OFF (outer surface)
2021-05-12 01:32:29 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:32:29 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:32:29 [DEBUG] Loading ..74%
2021-05-12 01:32:29 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:32:31 [DEBUG] Loading ..99%
2021-05-12 01:32:31 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:32:31 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:32:32 [DEBUG] 0% done
2021-05-12 01:32:32 [DEBUG] Testing for intersections ...
2021-05-12 01:32:35 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:32:35 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:32:35 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:32:35 [DEBUG] Loading ..74%
2021-05-12 01:32:35 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:32:37 [DEBUG] Loading ..99%
2021-05-12 01:32:37 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:32:37 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:32:37 [DEBUG] 0% done
2021-05-12 01:32:37 [DEBUG] Testing for intersections ...
2021-05-12 01:32:40 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:32:40 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_CAVITIES5.OFF (inner surface)
2021-05-12 01:32:43 [DEBUG] Cleaning FIXED_CAVITIES5.OFF (inner surface)
2021-05-12 01:32:43 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off"
2021-05-12 01:32:43 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:32:43 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:32:43 [DEBUG] Uniform remeshing ...
2021-05-12 01:32:43 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:32:43 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off'
2021-05-12 01:32:43 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off"
2021-05-12 01:32:43 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:32:43 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:32:43 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:32:43 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off'
2021-05-12 01:32:43 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:32:43 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:32:43 [DEBUG] Loading ..74%
2021-05-12 01:32:43 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:32:46 [DEBUG] Loading ..99%
2021-05-12 01:32:46 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:32:46 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:32:46 [DEBUG] 0% done
2021-05-12 01:32:46 [DEBUG] Testing for intersections ...
2021-05-12 01:32:49 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:32:49 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:32:49 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:32:49 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:32:49 [DEBUG] Loading ..74%
2021-05-12 01:32:49 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:32:50 [DEBUG] Loading ..99%
2021-05-12 01:32:50 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:32:50 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:32:50 [DEBUG] 0% done
2021-05-12 01:32:50 [DEBUG] Testing for intersections ...
2021-05-12 01:32:52 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:32:52 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:32:52 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off
2021-05-12 01:32:52 [DEBUG] Loading ..74%
2021-05-12 01:32:52 [DEBUG] INFO- Loaded 670 vertices and 1336 faces.
2021-05-12 01:32:54 [DEBUG] Loading ..99%
2021-05-12 01:32:54 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:32:54 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:32:54 [DEBUG] 0% done
2021-05-12 01:32:54 [DEBUG] Testing for intersections ...
2021-05-12 01:32:57 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:32:57 [INFO ] Decoupling fixed_cavities6 from CSF
2021-05-12 01:32:57 [DEBUG] Decoupling FIXED_CAVITIES6.OFF (surface 1) from FIXED_CSF1.OFF (surface 2)
2021-05-12 01:32:57 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:32:57 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:32:57 [DEBUG] Loading ..0%
2021-05-12 01:32:57 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:32:59 [DEBUG] Loading ..99%
2021-05-12 01:32:59 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:32:59 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:32:59 [DEBUG] 0% done
2021-05-12 01:32:59 [DEBUG] Testing for intersections ...
2021-05-12 01:33:00 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:33:00 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:33:00 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:33:00 [DEBUG] Loading ..0%
2021-05-12 01:33:00 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:33:02 [DEBUG] Loading ..99%
2021-05-12 01:33:02 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:33:02 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:33:02 [DEBUG] 0% done
2021-05-12 01:33:02 [DEBUG] Testing for intersections ...
2021-05-12 01:33:03 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:33:03 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_CAVITIES6.OFF (surface 1)
2021-05-12 01:33:04 [DEBUG] Moved 1.0 of 305 vertices
2021-05-12 01:33:04 [DEBUG] Cleaning FIXED_CAVITIES6.OFF (surface 1)
2021-05-12 01:33:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off"
2021-05-12 01:33:04 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:33:04 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:33:04 [DEBUG] Uniform remeshing ...
2021-05-12 01:33:04 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:33:04 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off'
2021-05-12 01:33:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off"
2021-05-12 01:33:04 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:33:04 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:33:04 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:33:04 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off'
2021-05-12 01:33:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:33:05 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:33:05 [DEBUG] Loading ..0%
2021-05-12 01:33:05 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:33:06 [DEBUG] Loading ..99%
2021-05-12 01:33:06 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:33:06 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:33:06 [DEBUG] 0% done
2021-05-12 01:33:06 [DEBUG] Testing for intersections ...
2021-05-12 01:33:07 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:33:07 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:33:07 [INFO ] Decoupling fixed_cavities6 from bone
2021-05-12 01:33:07 [DEBUG] Decoupling FIXED_CAVITIES6.OFF (inner surface) from FIXED_BONE1.OFF (outer surface)
2021-05-12 01:33:07 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:33:07 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:33:08 [DEBUG] Loading ..0%
2021-05-12 01:33:08 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:33:10 [DEBUG] Loading ..99%
2021-05-12 01:33:10 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:33:10 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:33:10 [DEBUG] 0% done
2021-05-12 01:33:10 [DEBUG] Testing for intersections ...
2021-05-12 01:33:13 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:33:13 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:33:13 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:33:13 [DEBUG] Loading ..0%
2021-05-12 01:33:13 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:33:15 [DEBUG] Loading ..99%
2021-05-12 01:33:15 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:33:15 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:33:16 [DEBUG] 0% done
2021-05-12 01:33:16 [DEBUG] Testing for intersections ...
2021-05-12 01:33:19 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:33:19 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_CAVITIES6.OFF (inner surface)
2021-05-12 01:33:21 [DEBUG] Cleaning FIXED_CAVITIES6.OFF (inner surface)
2021-05-12 01:33:21 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off"
2021-05-12 01:33:21 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:33:21 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:33:21 [DEBUG] Uniform remeshing ...
2021-05-12 01:33:21 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:33:21 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off'
2021-05-12 01:33:21 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off"
2021-05-12 01:33:21 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:33:21 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:33:21 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:33:21 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off'
2021-05-12 01:33:21 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:33:21 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:33:22 [DEBUG] Loading ..0%
2021-05-12 01:33:22 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:33:24 [DEBUG] Loading ..99%
2021-05-12 01:33:24 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:33:24 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:33:24 [DEBUG] 0% done
2021-05-12 01:33:24 [DEBUG] Testing for intersections ...
2021-05-12 01:33:27 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:33:27 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:33:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --shells 2 --no-clean --intersect
2021-05-12 01:33:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:33:27 [DEBUG] Loading ..0%
2021-05-12 01:33:27 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:33:29 [DEBUG] Loading ..99%
2021-05-12 01:33:29 [DEBUG] INFO- Loaded 48119 vertices and 96234 faces.
2021-05-12 01:33:29 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off was joined.
2021-05-12 01:33:29 [DEBUG] 0% done
2021-05-12 01:33:29 [DEBUG] Testing for intersections ...
2021-05-12 01:33:30 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:33:30 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:33:30 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off
2021-05-12 01:33:30 [DEBUG] Loading ..0%
2021-05-12 01:33:30 [DEBUG] INFO- Loaded 305 vertices and 610 faces.
2021-05-12 01:33:32 [DEBUG] Loading ..99%
2021-05-12 01:33:32 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:33:32 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:33:32 [DEBUG] 0% done
2021-05-12 01:33:32 [DEBUG] Testing for intersections ...
2021-05-12 01:33:36 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:33:36 [INFO ] Voxelizing
2021-05-12 01:33:36 [DEBUG] Creating cavities.nii.gz from fixed_cavities1.off
2021-05-12 01:33:36 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 01:33:43 [DEBUG] Creating cavities.nii.gz from fixed_cavities2.off
2021-05-12 01:33:43 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 01:33:49 [DEBUG] Creating cavities.nii.gz from fixed_cavities3.off
2021-05-12 01:33:50 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 01:33:55 [DEBUG] Creating cavities.nii.gz from fixed_cavities4.off
2021-05-12 01:33:56 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 01:34:01 [DEBUG] Creating cavities.nii.gz from fixed_cavities5.off
2021-05-12 01:34:01 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 01:34:08 [DEBUG] Creating cavities.nii.gz from fixed_cavities6.off
2021-05-12 01:34:08 [DEBUG] Making splits in z direction, tracing in x
2021-05-12 01:34:13 [INFO ] INNER AIR CAVITIES processing time: 00:05:18
2021-05-12 01:34:13 [INFO ] Processing OUTER AIR CAVITIES
2021-05-12 01:34:13 [INFO ] ========================================================================
2021-05-12 01:34:13 [INFO ] Creating non-decoupled surfaces
2021-05-12 01:34:13 [INFO ] Preparing volume for meshing
2021-05-12 01:34:15 [INFO ] Extracting surface(s)
2021-05-12 01:34:15 [DEBUG] Generating surface mesh from mod_air_outer_relabel.nii.gz
2021-05-12 01:34:15 [DEBUG] Creating initial mesh
2021-05-12 01:34:17 [DEBUG] Keeping maximum 9 largest shell(s) with minimum area of 100
2021-05-12 01:34:17 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\mod_air_outer_relabel_mesh.off" -a 2.0 --no-clean -q --shells 9 --splitShells --shellMinArea 100 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel"
2021-05-12 01:34:17 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:17 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\mod_air_outer_relabel_mesh.off
2021-05-12 01:34:17 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:17 [DEBUG] Processing fixed_air_outer_relabel1.off
2021-05-12 01:34:17 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.stl"
2021-05-12 01:34:17 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:17 [DEBUG] Loading ..89%
2021-05-12 01:34:17 [DEBUG] INFO- Loaded 1114 vertices and 2228 faces.
2021-05-12 01:34:17 [DEBUG] 0% done
2021-05-12 01:34:17 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.stl'
2021-05-12 01:34:17 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 01:34:17 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off"
2021-05-12 01:34:18 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:18 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:18 [DEBUG] Uniform remeshing ...
2021-05-12 01:34:18 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:34:18 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off'
2021-05-12 01:34:18 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1_resampled.stl"
2021-05-12 01:34:18 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:18 [DEBUG] Loading ..97%
2021-05-12 01:34:18 [DEBUG] INFO- Loaded 515 vertices and 1026 faces.
2021-05-12 01:34:18 [DEBUG] 0% done
2021-05-12 01:34:18 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1_resampled.stl'
2021-05-12 01:34:18 [DEBUG] Cleaning
2021-05-12 01:34:18 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off"
2021-05-12 01:34:18 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:18 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:18 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:34:18 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off'
2021-05-12 01:34:18 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1_resampled_clean.stl"
2021-05-12 01:34:18 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:18 [DEBUG] Loading ..97%
2021-05-12 01:34:18 [DEBUG] INFO- Loaded 515 vertices and 1026 faces.
2021-05-12 01:34:19 [DEBUG] 0% done
2021-05-12 01:34:19 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1_resampled_clean.stl'
2021-05-12 01:34:19 [DEBUG] Smoothing 5 time(s)
2021-05-12 01:34:19 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off"
2021-05-12 01:34:19 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:19 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:19 [DEBUG] Loading ..97%
2021-05-12 01:34:19 [DEBUG] INFO- Loaded 515 vertices and 1026 faces.
2021-05-12 01:34:19 [DEBUG] 0% done
2021-05-12 01:34:19 [DEBUG] Smoothing 5 steps.
2021-05-12 01:34:19 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 01:34:19 [DEBUG] 80 % done - 1 steps left
2021-05-12 01:34:19 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off'
2021-05-12 01:34:19 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1_resampled_clean_smoothed.stl"
2021-05-12 01:34:19 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:19 [DEBUG] Loading ..97%
2021-05-12 01:34:19 [DEBUG] INFO- Loaded 515 vertices and 1026 faces.
2021-05-12 01:34:19 [DEBUG] 0% done
2021-05-12 01:34:19 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1_resampled_clean_smoothed.stl'
2021-05-12 01:34:19 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 01:34:19 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:19 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:19 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 01:34:19 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:19 [DEBUG] Loading ..97%
2021-05-12 01:34:19 [DEBUG] INFO- Loaded 515 vertices and 1026 faces.
2021-05-12 01:34:19 [DEBUG] 0% done
2021-05-12 01:34:19 [DEBUG] Removing Spikes.
2021-05-12 01:34:19 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:34:19 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:34:19 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:34:19 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:34:19 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:34:19 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:34:19 [DEBUG] 100% done
2021-05-12 01:34:19 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 1.840952 (105.478783 DEGs)
2021-05-12 01:34:19 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:34:19 [DEBUG] INFO- V: 511
2021-05-12 01:34:19 [DEBUG] INFO- E: 1527
2021-05-12 01:34:19 [DEBUG] INFO- T: 1018
2021-05-12 01:34:19 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:34:19 [DEBUG] INFO- Handles: 0.
2021-05-12 01:34:19 [DEBUG] INFO- Shells: 1.
2021-05-12 01:34:19 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 01:34:19 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1_resampled_clean_smoothed_spike.stl"
2021-05-12 01:34:20 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:20 [DEBUG] Loading ..97%
2021-05-12 01:34:20 [DEBUG] INFO- Loaded 515 vertices and 1026 faces.
2021-05-12 01:34:20 [DEBUG] 0% done
2021-05-12 01:34:20 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1_resampled_clean_smoothed_spike.stl'
2021-05-12 01:34:20 [DEBUG] Uniform remeshing
2021-05-12 01:34:20 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off"
2021-05-12 01:34:20 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:20 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:20 [DEBUG] Uniform remeshing ...
2021-05-12 01:34:20 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:34:20 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off'
2021-05-12 01:34:20 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 01:34:20 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:20 [DEBUG] Loading ..97%
2021-05-12 01:34:20 [DEBUG] INFO- Loaded 515 vertices and 1026 faces.
2021-05-12 01:34:20 [DEBUG] 0% done
2021-05-12 01:34:20 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 01:34:20 [DEBUG] Cleaning
2021-05-12 01:34:20 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off"
2021-05-12 01:34:21 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:21 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:34:21 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:34:21 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off'
2021-05-12 01:34:21 [INFO ] Creating decoupled surfaces
2021-05-12 01:34:21 [INFO ] Preparing volume for meshing
2021-05-12 01:34:23 [INFO ] Extracting surface(s)
2021-05-12 01:34:23 [DEBUG] Generating surface mesh from mod_air_outer_decoupled.nii.gz
2021-05-12 01:34:23 [DEBUG] Creating initial mesh
2021-05-12 01:34:24 [DEBUG] Keeping maximum 9 largest shell(s) with minimum area of 100
2021-05-12 01:34:24 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\mod_air_outer_decoupled_mesh.off" -a 2.0 --no-clean -q --shells 9 --splitShells --shellMinArea 100 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled"
2021-05-12 01:34:25 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:25 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\mod_air_outer_decoupled_mesh.off
2021-05-12 01:34:25 [DEBUG] Saving output mesh to C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:25 [DEBUG] Processing fixed_air_outer_decoupled1.off
2021-05-12 01:34:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.stl"
2021-05-12 01:34:25 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:25 [DEBUG] Loading ..56%
2021-05-12 01:34:25 [DEBUG] INFO- Loaded 888 vertices and 1776 faces.
2021-05-12 01:34:25 [DEBUG] 0% done
2021-05-12 01:34:25 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.stl'
2021-05-12 01:34:25 [DEBUG] Resampling to a vertex density of 0.5
2021-05-12 01:34:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" -a 2.0 -u 5 -q --vertexDensity 0.5 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off"
2021-05-12 01:34:25 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:25 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:25 [DEBUG] Uniform remeshing ...
2021-05-12 01:34:25 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:34:25 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off'
2021-05-12 01:34:25 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1_resampled.stl"
2021-05-12 01:34:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:26 [DEBUG] Loading ..0%
2021-05-12 01:34:26 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:34:26 [DEBUG] 0% done
2021-05-12 01:34:26 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1_resampled.stl'
2021-05-12 01:34:26 [DEBUG] Cleaning
2021-05-12 01:34:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off"
2021-05-12 01:34:26 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:26 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:34:26 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off'
2021-05-12 01:34:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1_resampled_clean.stl"
2021-05-12 01:34:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:26 [DEBUG] Loading ..0%
2021-05-12 01:34:26 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:34:26 [DEBUG] 0% done
2021-05-12 01:34:26 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1_resampled_clean.stl'
2021-05-12 01:34:26 [DEBUG] Smoothing 5 time(s)
2021-05-12 01:34:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" -a 2.0 --taubin 5 --no-clean -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off"
2021-05-12 01:34:26 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:26 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:26 [DEBUG] Loading ..0%
2021-05-12 01:34:26 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:34:26 [DEBUG] 0% done
2021-05-12 01:34:26 [DEBUG] Smoothing 5 steps.
2021-05-12 01:34:26 [DEBUG] INFO- Lambda: 0.500000
2021-05-12 01:34:26 [DEBUG] 80 % done - 1 steps left
2021-05-12 01:34:26 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off'
2021-05-12 01:34:26 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1_resampled_clean_smoothed.stl"
2021-05-12 01:34:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:27 [DEBUG] Loading ..0%
2021-05-12 01:34:27 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:34:27 [DEBUG] 0% done
2021-05-12 01:34:27 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1_resampled_clean_smoothed.stl'
2021-05-12 01:34:27 [DEBUG] Removing Spikes with curvature parameter 5.0
2021-05-12 01:34:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" -a 2.0 --removeSpikes 5.0 -o C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:27 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:27 [DEBUG] INFO- spike removal threshold set to 5.000000
2021-05-12 01:34:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:27 [DEBUG] Loading ..0%
2021-05-12 01:34:27 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:34:27 [DEBUG] 0% done
2021-05-12 01:34:27 [DEBUG] Removing Spikes.
2021-05-12 01:34:27 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:34:27 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:34:27 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:34:27 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:34:27 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:34:27 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:34:27 [DEBUG] 100% done
2021-05-12 01:34:27 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 1.441329 (82.582058 DEGs)
2021-05-12 01:34:27 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:34:27 [DEBUG] INFO- V: 420
2021-05-12 01:34:27 [DEBUG] INFO- E: 1254
2021-05-12 01:34:27 [DEBUG] INFO- T: 836
2021-05-12 01:34:27 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:34:27 [DEBUG] INFO- Handles: 0.
2021-05-12 01:34:27 [DEBUG] INFO- Shells: 1.
2021-05-12 01:34:27 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni.off'
2021-05-12 01:34:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1_resampled_clean_smoothed_spike.stl"
2021-05-12 01:34:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:27 [DEBUG] Loading ..0%
2021-05-12 01:34:27 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:34:27 [DEBUG] 0% done
2021-05-12 01:34:27 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1_resampled_clean_smoothed_spike.stl'
2021-05-12 01:34:27 [DEBUG] Uniform remeshing
2021-05-12 01:34:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off"
2021-05-12 01:34:27 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:27 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:27 [DEBUG] Uniform remeshing ...
2021-05-12 01:34:27 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:34:27 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off'
2021-05-12 01:34:27 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1_resampled_clean_smoothed_spike_remesh.stl"
2021-05-12 01:34:28 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:28 [DEBUG] Loading ..0%
2021-05-12 01:34:28 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:34:28 [DEBUG] 0% done
2021-05-12 01:34:28 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1_resampled_clean_smoothed_spike_remesh.stl'
2021-05-12 01:34:28 [DEBUG] Cleaning
2021-05-12 01:34:28 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off"
2021-05-12 01:34:28 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:28 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:28 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:34:28 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off'
2021-05-12 01:34:28 [INFO ] Decoupling
2021-05-12 01:34:28 [INFO ] Decoupling fixed_air_outer_decoupled1 from skin
2021-05-12 01:34:28 [DEBUG] Decoupling FIXED_AIR_OUTER_DECOUPLED1.OFF (inner surface) from FIXED_SKIN1.OFF (outer surface)
2021-05-12 01:34:28 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --shells 2 --no-clean --intersect
2021-05-12 01:34:28 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:28 [DEBUG] Loading ..0%
2021-05-12 01:34:28 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:34:31 [DEBUG] Loading ..99%
2021-05-12 01:34:31 [DEBUG] INFO- Loaded 92510 vertices and 185020 faces.
2021-05-12 01:34:31 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off was joined.
2021-05-12 01:34:31 [DEBUG] 0% done
2021-05-12 01:34:31 [DEBUG] Testing for intersections ...
2021-05-12 01:34:33 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:34:33 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --shells 2 --no-clean --intersect
2021-05-12 01:34:33 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:33 [DEBUG] Loading ..0%
2021-05-12 01:34:33 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:34:36 [DEBUG] Loading ..99%
2021-05-12 01:34:36 [DEBUG] INFO- Loaded 92510 vertices and 185020 faces.
2021-05-12 01:34:36 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off was joined.
2021-05-12 01:34:36 [DEBUG] 0% done
2021-05-12 01:34:36 [DEBUG] Testing for intersections ...
2021-05-12 01:34:38 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:34:38 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_AIR_OUTER_DECOUPLED1.OFF (inner surface)
2021-05-12 01:34:41 [DEBUG] Cleaning FIXED_AIR_OUTER_DECOUPLED1.OFF (inner surface)
2021-05-12 01:34:41 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off"
2021-05-12 01:34:41 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:41 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:41 [DEBUG] Uniform remeshing ...
2021-05-12 01:34:41 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:34:41 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off'
2021-05-12 01:34:41 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off"
2021-05-12 01:34:41 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:41 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:41 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:34:41 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off'
2021-05-12 01:34:41 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --shells 2 --no-clean --intersect
2021-05-12 01:34:41 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:42 [DEBUG] Loading ..0%
2021-05-12 01:34:42 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:34:44 [DEBUG] Loading ..99%
2021-05-12 01:34:44 [DEBUG] INFO- Loaded 92510 vertices and 185020 faces.
2021-05-12 01:34:44 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off was joined.
2021-05-12 01:34:44 [DEBUG] 0% done
2021-05-12 01:34:44 [DEBUG] Testing for intersections ...
2021-05-12 01:34:47 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:34:47 [DEBUG] Total iterations needed for decoupling: 0
2021-05-12 01:34:47 [INFO ] Decoupling fixed_air_outer_decoupled1 from bone
2021-05-12 01:34:47 [DEBUG] Decoupling FIXED_AIR_OUTER_DECOUPLED1.OFF (surface 1) from FIXED_BONE1.OFF (surface 2)
2021-05-12 01:34:47 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:34:47 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:47 [DEBUG] Loading ..0%
2021-05-12 01:34:47 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:34:49 [DEBUG] Loading ..99%
2021-05-12 01:34:49 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:34:49 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:34:49 [DEBUG] 0% done
2021-05-12 01:34:49 [DEBUG] Testing for intersections ...
2021-05-12 01:34:53 [DEBUG] INFO- 25 intersecting triangles have been selected.
2021-05-12 01:34:53 [DEBUG] Iteration 1
2021-05-12 01:34:53 [DEBUG] Decoupling
2021-05-12 01:34:53 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" -a 2.0 --shells 2 --decouple-outin 0 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off"
2021-05-12 01:34:53 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:34:53 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:34:53 [DEBUG] Loading ..0%
2021-05-12 01:34:53 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:34:55 [DEBUG] Loading ..99%
2021-05-12 01:34:55 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:34:55 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:35:04 [DEBUG] 0% done
2021-05-12 01:35:04 [DEBUG] Decoupling first (outer) component from second one (move inwards). Min. distance: -1.
2021-05-12 01:35:04 [DEBUG] INFO- Iteration 1
2021-05-12 01:35:06 [DEBUG] INFO- 25 intersecting triangles have been selected.
2021-05-12 01:35:07 [DEBUG] INFO- Number of triangles inside: 15
2021-05-12 01:35:08 [DEBUG] INFO- Iteration 2
2021-05-12 01:35:11 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:35:12 [DEBUG] INFO- Number of triangles inside: 0
2021-05-12 01:35:12 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:35:12 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:35:12 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:35:12 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:35:12 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:35:12 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:35:12 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 1.354194 (77.589625 DEGs)
2021-05-12 01:35:12 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:35:12 [DEBUG] INFO- V: 424
2021-05-12 01:35:12 [DEBUG] INFO- E: 1266
2021-05-12 01:35:12 [DEBUG] INFO- T: 844
2021-05-12 01:35:12 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:35:12 [DEBUG] INFO- Handles: 0.
2021-05-12 01:35:12 [DEBUG] INFO- Shells: 1.
2021-05-12 01:35:12 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off'
2021-05-12 01:35:12 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:35:12 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:35:12 [DEBUG] Loading ..0%
2021-05-12 01:35:12 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:35:14 [DEBUG] Loading ..99%
2021-05-12 01:35:14 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:35:14 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:35:14 [DEBUG] 0% done
2021-05-12 01:35:14 [DEBUG] Testing for intersections ...
2021-05-12 01:35:18 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:35:18 [DEBUG] Cutting FIXED_AIR_OUTER_DECOUPLED1.OFF (surface 1)
2021-05-12 01:35:18 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" -a 2.0 --shells 2 --cut-inner 0 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off"
2021-05-12 01:35:18 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:35:18 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:35:18 [DEBUG] Loading ..0%
2021-05-12 01:35:18 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:35:20 [DEBUG] Loading ..99%
2021-05-12 01:35:20 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:35:20 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:35:29 [DEBUG] 0% done
2021-05-12 01:35:29 [DEBUG] Cutting triangles of the first component away, that are inside of the second one; Fill holes.
2021-05-12 01:35:31 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:35:33 [DEBUG] INFO- Number of triangles inside: 0
2021-05-12 01:35:33 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:35:33 [DEBUG] INFO- V: 424
2021-05-12 01:35:33 [DEBUG] INFO- E: 1266
2021-05-12 01:35:33 [DEBUG] INFO- T: 844
2021-05-12 01:35:33 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:35:33 [DEBUG] INFO- Handles: 0.
2021-05-12 01:35:33 [DEBUG] INFO- Shells: 1.
2021-05-12 01:35:33 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:35:33 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:35:33 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:35:33 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:35:33 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:35:33 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 1.354194 (77.589625 DEGs)
2021-05-12 01:35:33 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:35:33 [DEBUG] INFO- V: 424
2021-05-12 01:35:33 [DEBUG] INFO- E: 1266
2021-05-12 01:35:33 [DEBUG] INFO- T: 844
2021-05-12 01:35:33 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:35:33 [DEBUG] INFO- Handles: 0.
2021-05-12 01:35:33 [DEBUG] INFO- Shells: 1.
2021-05-12 01:35:33 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:35:33 [DEBUG] INFO- *** Cleaning iteration 0 ***
2021-05-12 01:35:33 [DEBUG] INFO- Removing degeneracies...
2021-05-12 01:35:33 [DEBUG] INFO- Removing self-intersections (using advanced method)...
2021-05-12 01:35:33 [DEBUG] INFO- Stage: Remove and Fill (1)
2021-05-12 01:35:33 [DEBUG] INFO- No intersecting triangles detected (in selection).
2021-05-12 01:35:33 [DEBUG] INFO- checkGeometry: minimum dihedral angle = 1.354194 (77.589625 DEGs)
2021-05-12 01:35:33 [DEBUG] INFO- *** Triangulation Report ***
2021-05-12 01:35:33 [DEBUG] INFO- V: 424
2021-05-12 01:35:33 [DEBUG] INFO- E: 1266
2021-05-12 01:35:33 [DEBUG] INFO- T: 844
2021-05-12 01:35:33 [DEBUG] INFO- Boundary: 0 components.
2021-05-12 01:35:33 [DEBUG] INFO- Handles: 0.
2021-05-12 01:35:33 [DEBUG] INFO- Shells: 1.
2021-05-12 01:35:33 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off'
2021-05-12 01:35:33 [DEBUG] Cleaning FIXED_AIR_OUTER_DECOUPLED1.OFF (surface 1)
2021-05-12 01:35:33 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off"
2021-05-12 01:35:33 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:35:33 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:35:33 [DEBUG] Uniform remeshing ...
2021-05-12 01:35:33 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:35:33 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off'
2021-05-12 01:35:33 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off"
2021-05-12 01:35:33 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:35:33 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:35:33 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:35:33 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off'
2021-05-12 01:35:33 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:35:33 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:35:33 [DEBUG] Loading ..0%
2021-05-12 01:35:33 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:35:36 [DEBUG] Loading ..99%
2021-05-12 01:35:36 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:35:36 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:35:36 [DEBUG] 0% done
2021-05-12 01:35:36 [DEBUG] Testing for intersections ...
2021-05-12 01:35:39 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:35:39 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:35:39 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:35:39 [DEBUG] Loading ..0%
2021-05-12 01:35:39 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:35:41 [DEBUG] Loading ..99%
2021-05-12 01:35:41 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:35:41 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:35:41 [DEBUG] 0% done
2021-05-12 01:35:41 [DEBUG] Testing for intersections ...
2021-05-12 01:35:45 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:35:45 [DEBUG] Attempting to ensure a minimum distance of 0.5 between surfaces by shrinking FIXED_AIR_OUTER_DECOUPLED1.OFF (surface 1)
2021-05-12 01:35:47 [DEBUG] Moved 171.0 of 424 vertices
2021-05-12 01:35:47 [DEBUG] Cleaning FIXED_AIR_OUTER_DECOUPLED1.OFF (surface 1)
2021-05-12 01:35:47 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" -a 2.0 -u 1 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off"
2021-05-12 01:35:47 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:35:47 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:35:47 [DEBUG] Uniform remeshing ...
2021-05-12 01:35:47 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:35:47 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off'
2021-05-12 01:35:47 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" -a 2.0 -q -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off"
2021-05-12 01:35:47 [DEBUG] Fixing asin tolerance to 3.491368e-02
2021-05-12 01:35:47 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:35:47 [DEBUG] Cleaning intersections, degeneracies ...
2021-05-12 01:35:47 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off'
2021-05-12 01:35:47 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:35:47 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:35:48 [DEBUG] Loading ..0%
2021-05-12 01:35:48 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:35:50 [DEBUG] Loading ..99%
2021-05-12 01:35:50 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:35:50 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:35:50 [DEBUG] 0% done
2021-05-12 01:35:50 [DEBUG] Testing for intersections ...
2021-05-12 01:35:53 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:35:53 [DEBUG] Total iterations needed for decoupling: 1
2021-05-12 01:35:53 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --shells 2 --no-clean --intersect
2021-05-12 01:35:53 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:35:53 [DEBUG] Loading ..0%
2021-05-12 01:35:53 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:35:55 [DEBUG] Loading ..99%
2021-05-12 01:35:55 [DEBUG] INFO- Loaded 76554 vertices and 153252 faces.
2021-05-12 01:35:55 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off was joined.
2021-05-12 01:35:56 [DEBUG] 0% done
2021-05-12 01:35:56 [DEBUG] Testing for intersections ...
2021-05-12 01:35:59 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:35:59 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --shells 2 --no-clean --intersect
2021-05-12 01:35:59 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:35:59 [DEBUG] Loading ..0%
2021-05-12 01:35:59 [DEBUG] INFO- Loaded 424 vertices and 844 faces.
2021-05-12 01:36:02 [DEBUG] Loading ..99%
2021-05-12 01:36:02 [DEBUG] INFO- Loaded 92510 vertices and 185020 faces.
2021-05-12 01:36:02 [DEBUG] INFO- C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off was joined.
2021-05-12 01:36:02 [DEBUG] 0% done
2021-05-12 01:36:02 [DEBUG] Testing for intersections ...
2021-05-12 01:36:04 [DEBUG] INFO- No intersecting triangles detected.
2021-05-12 01:36:04 [INFO ] OUTER AIR CAVITIES processing time: 00:01:50
2021-05-12 01:36:04 [INFO ] Converting surface meshes to STL
2021-05-12 01:36:04 [INFO ] ========================================================================
2021-05-12 01:36:04 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_wm.off" --no-clean -q --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\wm.stl"
2021-05-12 01:36:53 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_wm.off
2021-05-12 01:36:53 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\wm.stl'
2021-05-12 01:36:53 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_gm.off" --no-clean -q --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\gm.stl"
2021-05-12 01:37:34 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_gm.off
2021-05-12 01:37:34 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\gm.stl'
2021-05-12 01:37:34 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off" --no-clean -q --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\csf.stl"
2021-05-12 01:37:50 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_csf1.off
2021-05-12 01:37:50 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\csf.stl'
2021-05-12 01:37:50 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off" --no-clean -q --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\eyes.stl"
2021-05-12 01:37:51 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes1.off
2021-05-12 01:37:51 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\eyes.stl'
2021-05-12 01:37:51 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\eyes.stl" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_eyes2.off" -jc --shells 2 -q --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\eyes.stl"
2021-05-12 01:37:52 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\eyes.stl
2021-05-12 01:37:52 [DEBUG]
2021-05-12 01:37:52 [DEBUG] Joining input components ...
2021-05-12 01:37:52 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\eyes.stl'
2021-05-12 01:37:52 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off" --no-clean -q --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\bone.stl"
2021-05-12 01:38:17 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_bone1.off
2021-05-12 01:38:17 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\bone.stl'
2021-05-12 01:38:17 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off" --no-clean -q --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\skin.stl"
2021-05-12 01:38:47 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_skin1.off
2021-05-12 01:38:47 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\skin.stl'
2021-05-12 01:38:47 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_ventricles1.off" --no-clean -q --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\ventricles.stl"
2021-05-12 01:38:50 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_ventricles1.off
2021-05-12 01:38:50 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\ventricles.stl'
2021-05-12 01:38:50 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off" --no-clean -q --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl"
2021-05-12 01:38:51 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities1.off
2021-05-12 01:38:51 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl'
2021-05-12 01:38:51 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities2.off" -jc --shells 6 -q --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl"
2021-05-12 01:38:52 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl
2021-05-12 01:38:52 [DEBUG]
2021-05-12 01:38:52 [DEBUG] Joining input components ...
2021-05-12 01:38:52 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl'
2021-05-12 01:38:52 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities3.off" -jc --shells 6 -q --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl"
2021-05-12 01:38:54 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl
2021-05-12 01:38:54 [DEBUG]
2021-05-12 01:38:54 [DEBUG] Joining input components ...
2021-05-12 01:38:54 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl'
2021-05-12 01:38:54 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities4.off" -jc --shells 6 -q --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl"
2021-05-12 01:38:56 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl
2021-05-12 01:38:56 [DEBUG]
2021-05-12 01:38:56 [DEBUG] Joining input components ...
2021-05-12 01:38:56 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl'
2021-05-12 01:38:56 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities5.off" -jc --shells 6 -q --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl"
2021-05-12 01:38:59 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl
2021-05-12 01:38:59 [DEBUG]
2021-05-12 01:38:59 [DEBUG] Joining input components ...
2021-05-12 01:38:59 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl'
2021-05-12 01:38:59 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_cavities6.off" -jc --shells 6 -q --no-clean --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl"
2021-05-12 01:39:02 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl
2021-05-12 01:39:02 [DEBUG]
2021-05-12 01:39:02 [DEBUG] Joining input components ...
2021-05-12 01:39:02 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\cavities.stl'
2021-05-12 01:39:02 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off" --no-clean -q --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\air_outer_relabel.stl"
2021-05-12 01:39:02 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_relabel1.off
2021-05-12 01:39:02 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\air_outer_relabel.stl'
2021-05-12 01:39:02 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\meshfix" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off" --no-clean -q --stl -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\air_outer_decoupled.stl"
2021-05-12 01:39:03 [DEBUG] meshfix C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\tmp\fixed_air_outer_decoupled1.off
2021-05-12 01:39:03 [DEBUG] Saving output mesh to 'C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\air_outer_decoupled.stl'
2021-05-12 01:39:03 [INFO ] Done
2021-05-12 01:39:03 [INFO ] Conversion time: 00:02:59
2021-05-12 01:39:03 [INFO ] ========================================================================
2021-05-12 01:39:03 [INFO ] Surface meshing time: 00:45:26
2021-05-12 01:39:03 [INFO ] ========================================================================
2021-05-12 01:39:03 [INFO ] GENERATING VOLUME MESH
2021-05-12 01:39:03 [INFO ] ========================================================================
2021-05-12 01:39:03 [INFO ] Creating .geo file
2021-05-12 01:39:03 [INFO ] Creating volume mesh using Gmsh
2021-05-12 01:39:03 [INFO ] ========================================================================
2021-05-12 01:39:03 [DEBUG] Running "C:\Users\SONY\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\bin\win\gmsh" -3 -bin -format msh2 -o "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\MCI_PAPER.msh" "C:\Users\SONY\SimNIBS-3.2\adni data\MCI_PAPER\m2m_MCI_PAPER\MCI_PAPER.geo"