<HTML><HEAD><TITLE>headreco report</TITLE></HEAD><BODY><pre>2021-05-22 17:31:11 [DEBUG] /home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py all firstCase T1_curry.nii T2_T1space.nii
2021-05-22 17:31:11 [INFO ] ========================================================================
2021-05-22 17:31:11 [INFO ] PREPARING VOLUMES FOR MESHING
2021-05-22 17:31:11 [INFO ] ========================================================================
2021-05-22 17:31:11 [INFO ] Copying input files to m2m_firstCase
2021-05-22 17:31:17 [INFO ] Copying T1fs.nii.gz to T1fs_conform.nii.gz
2021-05-22 17:31:18 [INFO ] Preparing to segment
2021-05-22 17:31:19 [INFO ] Starting MATLAB
2021-05-22 17:31:19 [INFO ] ========================================================================
2021-05-22 17:31:19 [DEBUG] Running matlab -nosplash -nodesktop -r "addpath('/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/msh','/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/resources/spm12');try,segment_SPM('/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/resources/templates','/media/kaiser/My Book/Fabian/FirstCase/original_data/m2m_firstCase/segment/spm/T1fs_conform.nii','/media/kaiser/My Book/Fabian/FirstCase/original_data/m2m_firstCase/segment/spm/T2.nii',0.01,3,0); segment_CAT('/media/kaiser/My Book/Fabian/FirstCase/original_data/m2m_firstCase/segment/cat/T1fs_conform.nii','/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/resources/templates',1);catch ME,rethrow(ME);end,exit;"
2021-05-22 17:31:19 [INFO ] ---------------------------------------------------------------------------
2021-05-22 17:31:19 [INFO ] Warning: Cannot locate Java Runtime Environment (JRE) . . .
2021-05-22 17:31:19 [INFO ]
2021-05-22 17:31:19 [INFO ] 1. Either a correct JRE was not available for redistribution when
2021-05-22 17:31:19 [INFO ] this release was shipped, in which case you should refer to the
2021-05-22 17:31:19 [INFO ] Release Notes for additional information about how to get it.
2021-05-22 17:31:19 [INFO ]
2021-05-22 17:31:19 [INFO ] 2. Or you have tried to use the MATLAB_JAVA environment variable
2021-05-22 17:31:19 [INFO ] to specify an alternate JRE, but MATLAB cannot find it. Please
2021-05-22 17:31:19 [INFO ] run 'matlab -n' to determine what value you are using for
2021-05-22 17:31:19 [INFO ] MATLAB_JAVA and fix accordingly.
2021-05-22 17:31:19 [INFO ] ---------------------------------------------------------------------------
2021-05-22 17:31:19 [INFO ]
2021-05-22 17:31:19 [INFO ] matlab: No MATLAB bin directory for this machine architecture.
2021-05-22 17:31:19 [INFO ]
2021-05-22 17:31:19 [INFO ] ARCH = glnxa64
2021-05-22 17:31:19 [INFO ]
2021-05-22 17:31:19 [INFO ] Binarizing tissue probability maps
2021-05-22 17:31:19 [ERROR] Traceback (most recent call last):
File "/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 13, in <module>
main()
File "/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main
headmodel(sys.argv)
File "/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 265, in headmodel
raise OSError('Could not find tissue probability maps.\n'
OSError: Could not find tissue probability maps.
Probably something went wrong with the Matlab call or SPM
<HTML><HEAD><TITLE>headreco report</TITLE></HEAD><BODY><pre>2021-05-22 17:48:45 [DEBUG] /home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py all firstCase T1_curry.nii T2_T1space.nii
2021-05-22 17:48:45 [INFO ] ========================================================================
2021-05-22 17:48:45 [INFO ] PREPARING VOLUMES FOR MESHING
2021-05-22 17:48:45 [INFO ] ========================================================================
2021-05-22 17:48:45 [INFO ] Copying input files to m2m_firstCase
2021-05-22 17:48:48 [INFO ] Copying T1fs.nii.gz to T1fs_conform.nii.gz
2021-05-22 17:48:49 [INFO ] Preparing to segment
2021-05-22 17:48:49 [INFO ] Starting MATLAB
2021-05-22 17:48:49 [INFO ] ========================================================================
2021-05-22 17:48:49 [DEBUG] Running matlab -nosplash -nodesktop -r "addpath('/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/msh','/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/resources/spm12');try,segment_SPM('/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/resources/templates','/media/kaiser/My Book/Fabian/FirstCase/original_data/m2m_firstCase/segment/spm/T1fs_conform.nii','/media/kaiser/My Book/Fabian/FirstCase/original_data/m2m_firstCase/segment/spm/T2.nii',0.01,3,0); segment_CAT('/media/kaiser/My Book/Fabian/FirstCase/original_data/m2m_firstCase/segment/cat/T1fs_conform.nii','/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/resources/templates',1);catch ME,rethrow(ME);end,exit;"
2021-05-22 17:48:51 [INFO ] MATLAB is selecting SOFTWARE OPENGL rendering.
2021-05-22 17:49:10 [INFO ] [?1h=
2021-05-22 17:49:10 [INFO ] < M A T L A B (R) >
2021-05-22 17:49:10 [INFO ] Copyright 1984-2021 The MathWorks, Inc.
2021-05-22 17:49:10 [INFO ] R2021a (9.10.0.1602886) 64-bit (glnxa64)
2021-05-22 17:49:10 [INFO ] February 17, 2021
2021-05-22 17:49:10 [INFO ]
2021-05-22 17:49:11 [INFO ]
2021-05-22 17:49:11 [INFO ] To get started, type doc.
2021-05-22 17:49:11 [INFO ] For product information, visit www.mathworks.com.
2021-05-22 17:49:11 [INFO ]
2021-05-22 17:49:13 [INFO ] Bias regularization for T2 image : 1.000000e-02
2021-05-22 17:49:13 [INFO ] Downsampling factor for segmentation : 3
2021-05-22 17:49:13 [INFO ]
2021-05-22 17:49:26 [INFO ]
2021-05-22 17:49:26 [INFO ]
2021-05-22 17:49:26 [INFO ] ------------------------------------------------------------------------
2021-05-22 17:49:26 [INFO ] Running job #1
2021-05-22 17:49:26 [INFO ] ------------------------------------------------------------------------
2021-05-22 17:49:26 [INFO ] Running 'Coregister: Estimate & Reslice'
2021-05-22 17:49:26 [INFO ]
2021-05-22 17:49:26 [INFO ] SPM12: spm_coreg (v6435) 17:49:26 - 22/05/2021
2021-05-22 17:49:26 [INFO ] ========================================================================
2021-05-22 17:49:40 [INFO ] Completed : 17:49:40 - 22/05/2021
2021-05-22 17:49:40 [INFO ]
2021-05-22 17:49:40 [INFO ] SPM12: spm_reslice (v7141) 17:49:40 - 22/05/2021
2021-05-22 17:49:40 [INFO ] ========================================================================
2021-05-22 17:49:48 [INFO ] Completed : 17:49:48 - 22/05/2021
2021-05-22 17:49:48 [INFO ] Done 'Coregister: Estimate & Reslice'
2021-05-22 17:49:48 [INFO ] Running 'Segment'
2021-05-22 17:49:48 [INFO ]
2021-05-22 17:49:48 [INFO ] SPM12: spm_preproc_run (v6365) 17:49:48 - 22/05/2021
2021-05-22 17:49:48 [INFO ] ========================================================================
2021-05-22 17:49:51 [INFO ] [?1h=Segment /media/kaiser/My Book/Fabian/FirstCase/original_data/m2m_firstCase/segment/spm/T1fs_conform.nii
2021-05-22 17:56:57 [INFO ] Completed : 17:56:57 - 22/05/2021
2021-05-22 17:56:57 [INFO ] Done 'Segment'
2021-05-22 17:56:57 [INFO ] Running 'Normalise: Write'
2021-05-22 17:57:01 [INFO ] Done 'Normalise: Write'
2021-05-22 17:57:01 [INFO ] Running 'Deformations'
2021-05-22 17:57:03 [INFO ] spmprior_tissue 1,1,1
2021-05-22 17:57:04 [INFO ] spmprior_eye1 1,1,1
2021-05-22 17:57:06 [INFO ] spmprior_eye2 1,1,1
2021-05-22 17:57:08 [INFO ] spmprior_air 1,1,1
2021-05-22 17:57:09 [INFO ] spmprior_ventricles_lateral 1,1,1
2021-05-22 17:57:11 [INFO ] spmprior_spinal 1,1,1
2021-05-22 17:57:11 [INFO ] Done 'Deformations'
2021-05-22 17:57:11 [INFO ] Done
2021-05-22 17:57:11 [INFO ]
2021-05-22 17:57:11 [INFO ] Getting transformation matrices from MNI to subject space...
2021-05-22 17:57:11 [INFO ]
2021-05-22 17:57:11 [INFO ] SPM12: spm_coreg (v6435) 17:57:11 - 22/05/2021
2021-05-22 17:57:11 [INFO ] ========================================================================
2021-05-22 17:57:23 [INFO ] Completed : 17:57:23 - 22/05/2021
2021-05-22 17:57:27 [INFO ] Item extopts: No field(s) named
2021-05-22 17:57:27 [INFO ] darteltpm
2021-05-22 17:57:27 [INFO ] Item cat: No field(s) named
2021-05-22 17:57:27 [INFO ] extopts
2021-05-22 17:57:27 [INFO ]
2021-05-22 17:57:27 [INFO ]
2021-05-22 17:57:27 [INFO ] ------------------------------------------------------------------------
2021-05-22 17:57:27 [INFO ] Running job #1
2021-05-22 17:57:27 [INFO ] ------------------------------------------------------------------------
2021-05-22 17:57:27 [INFO ] Running 'CAT12: Segmentation'
2021-05-22 17:57:29 [INFO ]
2021-05-22 17:57:29 [INFO ] ------------------------------------------------------------------------
2021-05-22 17:57:29 [INFO ] CAT12 r1278: 1/1: ./m2m_firstCase/segment/cat/T1fs_conform.n
2021-05-22 17:57:29 [INFO ] ------------------------------------------------------------------------
2021-05-22 17:57:34 [INFO ] APPs bias correction:
2021-05-22 17:57:39 [INFO ] Preparation 4s
2021-05-22 17:58:02 [INFO ] SPM bias correction (samp: 6.00 mm, fwhm: 120 mm) bias= 9 mm 23s
2021-05-22 17:58:23 [INFO ] SPM bias correction (samp: 5.70 mm, fwhm: 105 mm) 21s
2021-05-22 17:58:44 [INFO ] SPM bias correction (samp: 5.40 mm, fwhm: 90 mm) 21s
2021-05-22 17:59:24 [INFO ] SPM bias correction (samp: 5.10 mm, fwhm: 75 mm) 40s
2021-05-22 18:00:04 [INFO ] SPM bias correction (samp: 4.80 mm, fwhm: 60 mm) 40s
2021-05-22 18:00:53 [INFO ] SPM bias correction (samp: 4.50 mm, fwhm: 45 mm) 49s
2021-05-22 18:01:04 [INFO ] Postprocessing 210s
2021-05-22 18:01:32 [INFO ] SANLM denoising (NCstr=-Inf): 27s
2021-05-22 18:01:41 [INFO ] Coarse affine registration: 9s
2021-05-22 18:01:49 [INFO ] Affine registration 8s
2021-05-22 18:03:31 [INFO ] SPM preprocessing 1 (estimate): 102s
2021-05-22 18:04:40 [INFO ] SPM preprocessing 2 (write): 70s
2021-05-22 18:04:56 [INFO ] Global intensity correction: 16s
2021-05-22 18:05:01 [INFO ] SANLM noise correction: 5s
2021-05-22 18:05:02 [INFO ] Local adaptive segmentation (LASstr=0.50):
2021-05-22 18:05:05 [INFO ] Prepare maps 3s
2021-05-22 18:05:07 [INFO ] Prepare partitions 2s
2021-05-22 18:05:16 [INFO ] Prepare segments (LASmod = 1.00) 9s
2021-05-22 18:05:54 [INFO ] Estimate local tissue thresholds 38s
2021-05-22 18:05:57 [INFO ] SANLM noise correction for LAS 3s
2021-05-22 18:05:57 [INFO ] 56s
2021-05-22 18:06:11 [INFO ] ROI segmentation (partitioning):
2021-05-22 18:06:16 [INFO ] Atlas -> subject space 5s
2021-05-22 18:06:19 [INFO ] Major structures 3s
2021-05-22 18:06:25 [INFO ] Ventricle detection 6s
2021-05-22 18:06:28 [INFO ] Blood vessel detection 2s
2021-05-22 18:06:35 [INFO ] WMH detection (WMHCstr=0.50) 7s
2021-05-22 18:06:35 [INFO ] Closing of deep structures 1s
2021-05-22 18:06:38 [INFO ] Side alignment 3s
2021-05-22 18:06:40 [INFO ] Final corrections 1s
2021-05-22 18:06:40 [INFO ] 29s
2021-05-22 18:06:41 [INFO ] Blood vessel correction (BVCstr=0.50): 1s
2021-05-22 18:06:41 [INFO ] Skull-stripping using graph-cut (gcutstr=0.50):
2021-05-22 18:06:43 [INFO ] WM initialisation 2s
2021-05-22 18:06:44 [INFO ] GM region growing 1s
2021-05-22 18:06:46 [INFO ] GM-CSF region growing 2s
2021-05-22 18:06:48 [INFO ] CSF region growing 2s
2021-05-22 18:06:50 [INFO ] Ventricle filling 2s
2021-05-22 18:06:50 [INFO ] 9s
2021-05-22 18:07:07 [INFO ] Amap using initial SPM12 segmentations (MRF filter strength 0.07): 14s
2021-05-22 18:07:07 [INFO ] AMAP peaks: [CSF,GM,WM] = [0.41±0.06,0.72±0.11,0.99±0.01]
2021-05-22 18:07:13 [INFO ] Final cleanup (gcutstr=0.50):
2021-05-22 18:07:16 [INFO ] Level 1 cleanup (ROI estimation) 3s
2021-05-22 18:07:17 [INFO ] Level 1 cleanup (brain masking) 1s
2021-05-22 18:07:17 [INFO ] Level 2 cleanup (CSF correction) 0s
2021-05-22 18:07:18 [INFO ] Level 3 cleanup (CSF/WM PVE) 1s
2021-05-22 18:07:18 [INFO ] 5s
2021-05-22 18:07:20 [INFO ] Internal WMH correction for spatial normalization (WMHCstr=0.50): 2s
2021-05-22 18:07:21 [INFO ]
2021-05-22 18:07:21 [INFO ]
2021-05-22 18:07:23 [INFO ] Dartel registration with 1.50 mm on a 1.50 mm Template:
2021-05-22 18:07:23 [INFO ] Template: "/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/resources/spm12/toolbox/cat12/templates_1.50mm/Template_1_IXI555_MNI152.nii"
2021-05-22 18:07:31 [INFO ] 1 | 0.1263 | 402253 0 402253 304.571
2021-05-22 18:07:38 [INFO ] 2 | 0.1076 | 342725 14475 357200 115.542
2021-05-22 18:07:41 [INFO ] 3 | 0.1046 | 333204 17610 350814 50.874
2021-05-22 18:07:48 [INFO ] 4 | 0.1035 | 329739 9739 339478 162.348
2021-05-22 18:07:53 [INFO ] 5 | 0.0965 | 307259 24061 331320 60.452
2021-05-22 18:07:56 [INFO ] 6 | 0.0961 | 305894 24547 330441 36.091
2021-05-22 18:08:05 [INFO ] 7 | 0.0964 | 306864 12788 319651 142.319
2021-05-22 18:08:10 [INFO ] 8 | 0.0886 | 282177 28621 310798 55.606
2021-05-22 18:08:16 [INFO ] 9 | 0.0882 | 280831 28766 309598 36.912
2021-05-22 18:08:26 [INFO ] 10 | 0.0882 | 280969 15157 296125 129.427
2021-05-22 18:08:33 [INFO ] 11 | 0.0800 | 254653 31413 286066 54.181
2021-05-22 18:08:39 [INFO ] 12 | 0.0793 | 252594 31866 284459 36.060
2021-05-22 18:08:53 [INFO ] 13 | 0.0793 | 252424 16797 269221 106.496
2021-05-22 18:09:03 [INFO ] 14 | 0.0722 | 229820 30304 260124 48.312
2021-05-22 18:09:13 [INFO ] 15 | 0.0714 | 227257 31324 258581 34.408
2021-05-22 18:09:30 [INFO ] 16 | 0.0711 | 226393 32828 259221 40.312
2021-05-22 18:09:44 [INFO ] 17 | 0.0707 | 225137 33173 258310 31.158
2021-05-22 18:09:57 [INFO ] 18 | 0.0704 | 224183 33790 257974 29.408
2021-05-22 18:10:06 [INFO ] 163s
2021-05-22 18:10:06 [INFO ] Jacobian determinant (RMS): 0.105447
2021-05-22 18:10:06 [INFO ] Template Matching: 0.070400
2021-05-22 18:10:16 [INFO ] Write result maps: 10s
2021-05-22 18:10:39 [INFO ] Surface and thickness estimation:
2021-05-22 18:10:39 [INFO ] lh:
2021-05-22 18:10:40 [INFO ] Thickness estimation (0.50 mm³):
2021-05-22 18:11:06 [INFO ] WM distance: 26s
2021-05-22 18:11:30 [INFO ] CSF distance: 23s
2021-05-22 18:11:47 [INFO ] PBT2x thickness: 18s
2021-05-22 18:11:48 [INFO ] Final Corrections: 0s
2021-05-22 18:11:53 [INFO ] 74s
2021-05-22 18:11:55 [INFO ] 76s
2021-05-22 18:12:14 [INFO ] Create initial surface 19s
2021-05-22 18:12:27 [INFO ] Reduce surface to 100000 faces: [?1h=[?1h=[?1h= 13s
2021-05-22 18:13:26 [INFO ] Topology correction and surface refinement: [?1h=[?1h=[?1h=[?1h= 59s
2021-05-22 18:13:26 [INFO ] Thickness / Depth mapping 0s
2021-05-22 18:13:29 [INFO ] Final correction of central surface in highly folded areas [?1h= 3s
2021-05-22 18:15:32 [INFO ] Spherical mapping with areal smoothing [?1h= 123s
2021-05-22 18:19:17 [INFO ] Spherical registration [?1h= 224s
2021-05-22 18:19:18 [INFO ] rh:
2021-05-22 18:19:19 [INFO ] Thickness estimation (0.50 mm³):
2021-05-22 18:19:43 [INFO ] WM distance: 24s
2021-05-22 18:20:07 [INFO ] CSF distance: 24s
2021-05-22 18:20:25 [INFO ] PBT2x thickness: 18s
2021-05-22 18:20:26 [INFO ] Final Corrections: 0s
2021-05-22 18:20:31 [INFO ] 73s
2021-05-22 18:20:33 [INFO ] 75s
2021-05-22 18:20:51 [INFO ] Create initial surface 18s
2021-05-22 18:21:04 [INFO ] Reduce surface to 100000 faces: [?1h=[?1h=[?1h= 13s
2021-05-22 18:21:56 [INFO ] Topology correction and surface refinement: [?1h=[?1h=[?1h=[?1h= 52s
2021-05-22 18:21:56 [INFO ] Thickness / Depth mapping 0s
2021-05-22 18:21:59 [INFO ] Final correction of central surface in highly folded areas [?1h= 3s
2021-05-22 18:24:07 [INFO ] Spherical mapping with areal smoothing [?1h= 128s
2021-05-22 18:28:25 [INFO ] Spherical registration [?1h= 258s
2021-05-22 18:28:25 [INFO ] Display thickness: /media/kaiser/My Book/Fabian/FirstCase/original_data/m2m_firstCase/segment/cat/surf/lh.thickness.T1fs_conform
2021-05-22 18:28:25 [INFO ] Display thickness: /media/kaiser/My Book/Fabian/FirstCase/original_data/m2m_firstCase/segment/cat/surf/rh.thickness.T1fs_conform
2021-05-22 18:28:25 [INFO ] Surface and thickness estimation: 1090s
2021-05-22 18:28:35 [INFO ] Quality check: 10s
2021-05-22 18:28:38 [INFO ] Done 'CAT12: Segmentation'
2021-05-22 18:28:38 [INFO ] Done
2021-05-22 18:28:38 [INFO ]
2021-05-22 18:28:38 [INFO ]
2021-05-22 18:28:38 [INFO ]
2021-05-22 18:28:38 [INFO ] ------------------------------------------------------------------------
2021-05-22 18:28:38 [INFO ] Running job #1
2021-05-22 18:28:38 [INFO ] ------------------------------------------------------------------------
2021-05-22 18:28:38 [INFO ] Running 'Deformations'
2021-05-22 18:28:40 [INFO ] cattemplate_CC_hammers 1,1,1
2021-05-22 18:28:41 [INFO ] cattemplate_brainstem_hammers 1,1,1
2021-05-22 18:28:42 [INFO ] cattemplate_cerebellum_hammers 1,1,1
2021-05-22 18:28:44 [INFO ] cattemplate_fornix_JHU 1,1,1
2021-05-22 18:28:45 [INFO ] cattemplate_ventricles_lateral_hammers 1,1,1
2021-05-22 18:28:46 [INFO ] cattemplate_ventricles_third_hammers 1,1,1
2021-05-22 18:28:48 [INFO ] cattemplate_thalamus_harvard 1,1,1
2021-05-22 18:28:50 [INFO ] Template_1_IXI555_MNI152 1,1,1 2,1,1
2021-05-22 18:28:50 [INFO ] Done 'Deformations'
2021-05-22 18:28:50 [INFO ] Done
2021-05-22 18:28:50 [INFO ]
2021-05-22 18:28:53 [INFO ] [?1l>
2021-05-22 18:28:53 [INFO ] Binarizing tissue probability maps
2021-05-22 18:29:02 [INFO ] Creating unity.xfm and ref_FS.nii.gz
2021-05-22 18:29:02 [ERROR] Traceback (most recent call last):
File "/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 13, in <module>
main()
File "/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main
headmodel(sys.argv)
File "/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 286, in headmodel
hmu.write_ref_fs(vols_conform[0])
File "/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/msh/hmutils.py", line 3454, in write_ref_fs
data = np.transpose(np.zeros_like(vol.get_data()),(0,2,1))
File "/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 639, in transpose
return _wrapfunc(a, 'transpose', axes)
File "/home/kaiser/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/numpy/core/fromnumeric.py", line 56, in _wrapfunc
return getattr(obj, method)(*args, **kwds)
ValueError: axes don't match array