From mrsnicolson at gmail.com Thu Apr 1 20:36:24 2021 From: mrsnicolson at gmail.com (Valerie Nicolson) Date: Thu, 1 Apr 2021 11:36:24 -0700 Subject: [Simnibs-discuss] T2 imaging protocol questions Message-ID: Hello all, Can anyone advise on the suitability of using a high resolution 3D T2 Flair sequence for headreco? A collaborator is already acquiring this in their study, and the output of headreco looks good to me (though I am no expert), and we are trying to figure out if they need to add a T2 to their protocol if we want to do electric field modeling. Also, on some older data, we have a low resolution T2 with brain coverage (not full head/face coverage like the T1). The GM, WM, CSF segmentation looks OK, but I get some very strange results for skin and bone. It looks like the skin of the subject superiorly (where there was both T1 and T2 coverage) and the skin of the template elsewhere (where there was T1 coverage only...see attached picture). The T1 and T2 look registered (if I compare T1fs_conform.nii.gz to T2_conform.nii.gz), and T1fs_nu_nonlin_MNI.nii looks registered to MNI152_T1_1mm.nii (using headreco check), but T1fs_nu_12DOF_MNI.nii is way off. Any thoughts? Thanks, Valerie Cardenas Nicolson Palo Alto VA [image: Screen Shot 2021-04-01 at 11.27.43 AM.png] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2021-04-01 at 11.27.43 AM.png Type: image/png Size: 593890 bytes Desc: not available URL: From oulap at drcmr.dk Tue Apr 6 08:19:27 2021 From: oulap at drcmr.dk (Oula) Date: Tue, 6 Apr 2021 08:19:27 +0200 Subject: [Simnibs-discuss] T2 imaging protocol questions In-Reply-To: References: Message-ID: <20210406062627.0FA784AA9AF@curie.drcmr.dk> Hi Valerie, If you?re planning to skip a T1w scan completely the answer is yes and no. You can create a headmodel with headreco using a FLAIR, and that will likely turn out fairly okay, but you cannot use the CAT12 toolbox (included in headreco) to create the middle cortical surface. CAT12 requires a T1 in order to work. So if you need the middle cortical surface to visualize the electric field or mapping onto the FreeSurfer average space then you should have a T1w scan. W.r.t. the T1/T2 it?s exactly as you described: the field-of-view is cropped to the smaller scan. So if the T2 only had the upper part of the head, the T1 will be masked to also only have the upper part of the head, and the masked/missing part is reconstructed from the template. Best, Oula L?hett?j?: Valerie Nicolson L?hetetty: 2. april 2021 09:42 Vastaanottaja: discuss at simnibs.org Aihe: [Simnibs-discuss] T2 imaging protocol questions Hello all, Can anyone advise on the suitability of using a high resolution 3D T2 Flair sequence for headreco? A collaborator is already acquiring this in their study, and the output of headreco looks good to me (though I am no expert), and we are trying to figure out if they need to add a T2 to their protocol if we want to do electric field modeling. Also, on some older data, we have a low resolution T2 with brain coverage (not full head/face coverage like the T1). The GM, WM, CSF segmentation looks OK, but I get some very strange results for skin and bone. It looks like the skin of the subject superiorly (where there was both T1 and T2 coverage) and the skin of the template elsewhere (where there was T1 coverage only...see attached picture). The T1 and T2 look registered (if I compare T1fs_conform.nii.gz to T2_conform.nii.gz), and T1fs_nu_nonlin_MNI.nii looks registered to MNI152_T1_1mm.nii (using headreco check), but T1fs_nu_12DOF_MNI.nii is way off. Any thoughts? Thanks, Valerie Cardenas Nicolson Palo Alto VA -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 6D662CB944C1472F8EAE39CBB9D884AB.png Type: image/png Size: 172571 bytes Desc: not available URL: From mrsnicolson at gmail.com Tue Apr 6 17:50:19 2021 From: mrsnicolson at gmail.com (Valerie Nicolson) Date: Tue, 6 Apr 2021 08:50:19 -0700 Subject: [Simnibs-discuss] T2 imaging protocol questions In-Reply-To: <606bff0e.1c69fb81.25890.ff58SMTPIN_ADDED_MISSING@mx.google.com> References: <606bff0e.1c69fb81.25890.ff58SMTPIN_ADDED_MISSING@mx.google.com> Message-ID: Thanks so much for your answer! We would be using a T1w with the T2-flair. When I ran headreco with both the headmodel looked very good, but wasn't sure what errors I might introduce by using the T2-flair instead of a T2. Valerie On Mon, Apr 5, 2021 at 11:26 PM Oula wrote: > Hi Valerie, > > > > If you?re planning to skip a T1w scan completely the answer is yes and no. > You can create a headmodel with headreco using a FLAIR, and that will > likely turn out fairly okay, but you cannot use the CAT12 toolbox (included > in headreco) to create the middle cortical surface. CAT12 requires a T1 in > order to work. So if you need the middle cortical surface to visualize the > electric field or mapping onto the FreeSurfer average space then you should > have a T1w scan. > > > > W.r.t. the T1/T2 it?s exactly as you described: the field-of-view is > cropped to the smaller scan. So if the T2 only had the upper part of the > head, the T1 will be masked to also only have the upper part of the head, > and the masked/missing part is reconstructed from the template. > > > > Best, > Oula > > > > *L?hett?j?: *Valerie Nicolson > *L?hetetty: *2. april 2021 09:42 > *Vastaanottaja: *discuss at simnibs.org > *Aihe: *[Simnibs-discuss] T2 imaging protocol questions > > > > Hello all, > > > > Can anyone advise on the suitability of using a high resolution 3D T2 > Flair sequence for headreco? A collaborator is already acquiring this in > their study, and the output of headreco looks good to me (though I am no > expert), and we are trying to figure out if they need to add a T2 to their > protocol if we want to do electric field modeling. > > > > Also, on some older data, we have a low resolution T2 with brain coverage > (not full head/face coverage like the T1). The GM, WM, CSF segmentation > looks OK, but I get some very strange results for skin and bone. It looks > like the skin of the subject superiorly (where there was both T1 and T2 > coverage) and the skin of the template elsewhere (where there was T1 > coverage only...see attached picture). The T1 and T2 look registered (if I > compare T1fs_conform.nii.gz to T2_conform.nii.gz), and > T1fs_nu_nonlin_MNI.nii looks registered to MNI152_T1_1mm.nii (using > headreco check), but T1fs_nu_12DOF_MNI.nii is way off. Any thoughts? > > > > Thanks, > > > > Valerie Cardenas Nicolson > > Palo Alto VA > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 6D662CB944C1472F8EAE39CBB9D884AB.png Type: image/png Size: 172571 bytes Desc: not available URL: From axelt at drcmr.dk Tue Apr 6 19:53:58 2021 From: axelt at drcmr.dk (Axel Thielscher) Date: Tue, 6 Apr 2021 19:53:58 +0200 Subject: [Simnibs-discuss] TI Simulation Visualization with SimNIBS In-Reply-To: References: Message-ID: Hi Connor, the TI.m saves the mesh with the TI field as 'ernie_TIenvelope.msh', which you can open in gmsh (see https://simnibs.github.io/simnibs/build/html/tutorial/visualization.html on an introduction on how to use it). To get some more information on focality and peak field strength in gray matter, you can add to the end of TI.m: *mesh_get_fieldpeaks_and_focality(mout,'field_idx',3);* To get a visualization of the regions in which the TI amplitude exceeds a certain threshold, you can add: *% show regions exceeding 95 percentile** **threshold = 0.143; % 95 percentile of the TI field in GM, as printed by mesh_get_fieldpeaks_and_focality** ** **tet_idx = mout.element_data{3}.tetdata>=threshold;** **m_vis=mesh_extract_regions(mout, 'elemtype','tet','region_idx',2,'tet_idx', tet_idx);** **TR = triangulation(m_vis.tetrahedra,m_vis.nodes(:,1),m_vis.nodes(:,2),m_vis.nodes(:,3));** **m_vis.triangles=freeBoundary(TR);** **m_vis.triangle_regions=ones(size(m_vis.triangles,1),1)*1002;** **mesh_show_surface(mout,'showSurface',true,'facealpha',0.4); % show the whole cortex semi-transparent** **mesh_show_surface(m_vis,'showSurface',true,'surfaceColor',[1 0 0],'haxis',gca); % add peak TI region in red * I hope, these hints help a bit. Best regards, Axel On 3/18/2021 5:49 AM, Moore, Connor Joseph wrote: > Hello, > > I'm Connor Moore, an undergraduate at the Pennsylvania State > University, and I'm currently investigating the potential use of > temporal interference to treat Parkinson's Disease patients. After > looking on the discussion board, I found a helpful email chain > ?that > contained a script that calculates the stimulation caused by TI with a > given electrode configuration. This script has been excellent for > giving me an estimate of the general area of the brain that will be > stimulated, but I was wondering if it would be possible to create a 3D > visualization of this data similar to the output of the tDCS example > scripts. > > Thank you for your time, and I hope to hear from you soon. > > Regards, > Connor > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -- Dr. Axel Thielscher Associate Professor Danish Research Center for Magnetic Resonance Copenhagen University Hospital Hvidovre DK-2650 Hvidovre, Denmark www.drcmr.dk & Department of Health Technology Technical University of Denmark DK-2800 Kgs. Lyngby http://www.healthtech.dtu.dk/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mpnblbngfbekglia.png Type: image/png Size: 835051 bytes Desc: not available URL: From oulap at drcmr.dk Mon Apr 12 13:05:57 2021 From: oulap at drcmr.dk (Oula) Date: Mon, 12 Apr 2021 13:05:57 +0200 Subject: [Simnibs-discuss] Benefit of including diffusion tensors inmodeling? In-Reply-To: References: Message-ID: <20210412111307.269154AA9AA@curie.drcmr.dk> Hi Daniel, Sorry for the late reply. Our Group has published one paper on this: https://www.sciencedirect.com/science/article/pii/S1053811911007154 Long story short, it does have an effect mostly in the White matter and the size of the effect depends on the coil orientation (for TMS). For gray matter the effect is not that large. Best, Oula L?hett?j?: Mccalley, Daniel L?hetetty: 26. marts 2021 14:47 Vastaanottaja: discuss at simnibs.org Aihe: [Simnibs-discuss] Benefit of including diffusion tensors inmodeling? Hi all,? I think you may have published on this question, so feel free to forward the literature if that's easier -- but you find there to be a substantial difference in efield models when diffusion tensors are included in the modeling?? Thanks! Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience -------------- next part -------------- An HTML attachment was scrubbed... URL: From etsheets at email.sc.edu Wed Apr 14 18:12:25 2021 From: etsheets at email.sc.edu (SHEETS, EMERSON T) Date: Wed, 14 Apr 2021 16:12:25 +0000 Subject: [Simnibs-discuss] Non-Human Mesh Inquiry Message-ID: Hello, My name is Emerson Sheets and I am working on a senior design project for the University of South Carolina utilizing SimNIBS to create a head mesh from a porcine MRI file. My group is running into difficulties where the headreco function is compressing our volumes of a porcine MRI to mimic that of a human. Is there any way to mitigate the headreco function from automatically conforming the porcine head to a human head by a command, boundary conditions, or some other means? Best, Emerson Sheets -------------- next part -------------- An HTML attachment was scrubbed... URL: From kirsten.gainsford at monash.edu Thu Apr 15 09:20:07 2021 From: kirsten.gainsford at monash.edu (Kirsten Gainsford) Date: Thu, 15 Apr 2021 17:20:07 +1000 Subject: [Simnibs-discuss] No ernie templates installed with SimNIBS program Message-ID: Hello, I have just downloaded the most recent version of SimNIBS for Mac to my Mac laptop and am having an issue where there are no "ernie" folders or files to be located in my version at all, preventing me from creating a leadfield. Is this a known issue? How do I resolve it? Thank you in advance. Kind Regards, Kirsten -- Kirsten Gainsford, PhD Candidate and Research* Assistant** Epworth Centre for Innovation in Mental Health (ECIMH) *Monash University and Epworth HealthCare* Faculty of Medicine, Nursing and Health Sciences Monash University 888 Toorak Road Camberwell VIC 3124 Melbourne, Australia * Research assistant hours: Mon, Tues and alternating Fri. e: kirsten.gainsford at monash.edu twitter: @KirstenGainsfo1 *I acknowledge the Traditional Owners and Custodians of the lands on which I live and work, the Boon Wurrung and Woiwurrung (Wurundjeri) peoples of the Kulin Nation, and pay my respect to Elders past, present and future.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From oulap at drcmr.dk Thu Apr 15 10:26:39 2021 From: oulap at drcmr.dk (Oula) Date: Thu, 15 Apr 2021 10:26:39 +0200 Subject: [Simnibs-discuss] No ernie templates installed with SimNIBS program In-Reply-To: References: Message-ID: <20210415083358.77B9D4AA955@curie.drcmr.dk> Hi Kirsten, You can download the example data from here: https://simnibs.github.io/simnibs/build/html/dataset.html Best, Oula L?hett?j?: Kirsten Gainsford L?hetetty: 15. april 2021 10:31 Vastaanottaja: discuss at simnibs.org Aihe: [Simnibs-discuss] No ernie templates installed with SimNIBS program Hello,? I have just downloaded the most recent version of SimNIBS for Mac to my Mac laptop and?am having an issue where there are no "ernie" folders or files to be located in my version at all, preventing me from creating a leadfield. Is this a known issue? How do I resolve it? Thank you in advance. Kind Regards, Kirsten -- Kirsten Gainsford,?PhD Candidate and?Research?Assistant* Epworth Centre for Innovation in Mental Health (ECIMH) Monash University and Epworth HealthCare Faculty of Medicine, Nursing and Health Sciences Monash University 888 Toorak Road Camberwell?VIC 3124 Melbourne,?Australia * Research assistant hours: Mon, Tues and alternating Fri.? e: kirsten.gainsford at monash.edu twitter: @KirstenGainsfo1 I acknowledge the Traditional Owners and Custodians of the lands on which I live and work, the Boon Wurrung and Woiwurrung (Wurundjeri) peoples of the Kulin Nation, and pay my respect to Elders past, present and future. -------------- next part -------------- An HTML attachment was scrubbed... URL: From 1534576032 at qq.com Mon Apr 19 10:42:52 2021 From: 1534576032 at qq.com (=?ISO-8859-1?B?bGVvcGFyZA==?=) Date: Mon, 19 Apr 2021 16:42:52 +0800 Subject: [Simnibs-discuss] install Message-ID: -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: install.log Type: application/octet-stream Size: 717801 bytes Desc: not available URL: From oulap at drcmr.dk Mon Apr 19 10:34:04 2021 From: oulap at drcmr.dk (Oula) Date: Mon, 19 Apr 2021 10:34:04 +0200 Subject: [Simnibs-discuss] Non-Human Mesh Inquiry In-Reply-To: References: Message-ID: <20210419084121.7DB584AB170@curie.drcmr.dk> Hi Emerson, Simnibs does not provide automated tools for generating tissue segmentations from porcine heads. However, if you are able to generate a segmentation into white matter, gray matter, CSF, skull and scalp, I can generate a FEM mesh for running the simulations. Best, Oula L?hett?j?: SHEETS, EMERSON T L?hetetty: 14. april 2021 18:40 Vastaanottaja: discuss at simnibs.org Aihe: [Simnibs-discuss] Non-Human Mesh Inquiry Hello, My name is Emerson Sheets and I am working on a senior design project for the University of South Carolina utilizing SimNIBS to create a head mesh from a porcine MRI file. My group is running into difficulties where the headreco function is compressing our volumes of a porcine MRI to mimic that of a human. Is there any way to mitigate the headreco function from automatically conforming the porcine head to a human head by a command, boundary conditions, or some other means? Best, Emerson Sheets -------------- next part -------------- An HTML attachment was scrubbed... URL: From benkiffer at hotmail.com Tue Apr 20 13:36:02 2021 From: benkiffer at hotmail.com (ben kiffer) Date: Tue, 20 Apr 2021 11:36:02 +0000 Subject: [Simnibs-discuss] Parameter of coils Message-ID: <265401E2-1CAB-4423-BA7B-30ECB66FF6CE@hotmail.com> Dear Ladies and Gentlemen, First, I want to give you a praise for Simnibs, the program has already helped me a lot in the field of transcranial magnetic stimulation and works perfectly. I wanted to ask if somehow there is the possibility to adjust parameters (no. of coils & diameter) of the coil (Magstim_70mm_Fig8. nii. gz), this would make my work much easier and would bring me much further. I would be very happy to hear an answer. With kind regards Ben Kiffer From d.j.l.g.schutter at uu.nl Wed Apr 21 22:07:58 2021 From: d.j.l.g.schutter at uu.nl (Schutter, D.J.L.G. (Dennis)) Date: Wed, 21 Apr 2021 20:07:58 +0000 Subject: [Simnibs-discuss] =?windows-1252?q?Error_value_=93axes_don=27t_ma?= =?windows-1252?q?tch_array=94?= Message-ID: Dear SimNIBS, First of all, thank you for the amazing program. I am struggling with creating a mesh (using headreco all) based on a NIFTI file that I converted from DICOM (with dicm2nii). While the first steps few steps in Matlab run successful, I get the error value ?axes don't match array? at the start of Binarizing tissue probability maps and program terminates (see below for complete message). When I run headreco all with Ernie?s NIFTI file the headreco all it works fine, so I guess something went wrong with the conversion, but I cannot put my finger on the problem. The scan is a standard 3T scan: voxel dimensions: 1x1x1mm and image (XYZ) dimensions: 192x256x256, and the NIFTI scan looks fine in MRICRO and MANGO. I hope you can help me. Thank you very much for your valuable time and I look forward to hearing from you. Best wishes, Dennis Binarizing tissue probability maps Creating unity.xfm and ref_FS.nii.gz Traceback (most recent call last): File "C:\Users\schut103\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\cli\headreco.py", line 13, in main() File "C:\Users\schut103\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\cli\headreco.py", line 10, in main headmodel(sys.argv) File "C:\Users\schut103\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\msh\headreco.py", line 286, in headmodel hmu.write_ref_fs(vols_conform[0]) File "C:\Users\schut103\SimNIBS-3.2\simnibs_env\lib\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 "C:\Users\schut103\SimNIBS-3.2\simnibs_env\lib\site-packages\numpy\core\fromnumeric.py", line 639, in transpose return _wrapfunc(a, 'transpose', axes) File "C:\Users\schut103\SimNIBS-3.2\simnibs_env\lib\site-packages\numpy\core\fromnumeric.py", line 56, in _wrapfunc return getattr(obj, method)(*args, **kwds) ValueError: axes don't match array -------------- next part -------------- An HTML attachment was scrubbed... URL: From hndnyaman at gmail.com Sat Apr 24 11:00:29 2021 From: hndnyaman at gmail.com (Handan Yaman) Date: Sat, 24 Apr 2021 12:00:29 +0300 Subject: [Simnibs-discuss] About Mesh File Message-ID: Dear Simnibs Team, To open the "S20_FL.msh" file in the application, I am encountering an error at https://filesender.surf.nl/?s=download&token=43ba5d13-923c-4606 b0f0-8c9f836424e1 (I shared a photo of it in the attachment). Therefore, I am unable to make progress. I want to get your information on this subject. Sincerely Handan YAMAN [image: error.png] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: error.png Type: image/png Size: 29370 bytes Desc: not available URL: From Susanna.Fryer at ucsf.edu Tue Apr 27 19:26:38 2021 From: Susanna.Fryer at ucsf.edu (Fryer, Susanna) Date: Tue, 27 Apr 2021 17:26:38 +0000 Subject: [Simnibs-discuss] targeting deep structure with known MNI coordinate Message-ID: Hello, We are trying to model a TMS target that is in deep medial prefrontal cortex/dorsal ACC, but are having trouble understanding how to navigate to our desired target, which we have defined in MNI. We are able to create models at the surface, but can't seem to navigate the software to go into cortex. Specifically, how do we convert our MNI coordinate to the coordinate system that SIMnibs is using (and what coordinate system is it that SIMnibs uses?). How do we target below the surface? Thank you so much for guidance! Susanna Fryer, UCSF -------------- next part -------------- An HTML attachment was scrubbed... URL: From Susanna.Fryer at ucsf.edu Wed Apr 28 05:52:17 2021 From: Susanna.Fryer at ucsf.edu (Fryer, Susanna) Date: Wed, 28 Apr 2021 03:52:17 +0000 Subject: [Simnibs-discuss] creating rTMS e-field model with a known MNI coordinate Message-ID: Hello, We are trying to model a TMS target that is in deep medial prefrontal cortex/dorsal ACC, but are having trouble understanding how to navigate to our desired target, which we have defined in MNI. We are able to create models at the surface, but can't seem to navigate the software to go into cortex. Specifically, how do we convert our MNI coordinate to the coordinate system that SIMnibs is using (and what coordinate system is it that SIMnibs uses?). How do we target below the surface? Thank you so much for guidance! -------------- next part -------------- An HTML attachment was scrubbed... URL: From tayebzaidi at gmail.com Thu Apr 29 02:30:21 2021 From: tayebzaidi at gmail.com (Tayeb Zaidi) Date: Wed, 28 Apr 2021 20:30:21 -0400 Subject: [Simnibs-discuss] Meshfix error in SimNIBS-3.2.3 Message-ID: Hello, I've been working to use SimNIBS-3.2 to generate head segmentation for several subjects from the Human Connectome Project. When running "mri2mesh --all subjectnumber T1w.nii T2w.nii" I successfully finish recon-all from Freesurfer and then the mri2mesh script raises an error when creating the subcortical mask. The exact error is: " mris_convert ./opticrad_FS.fsmesh ./opticrad_FS.stl /home/awarru/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix subcortical_FS.stl -a 2.0 --remove-handles -q -o subcortical.off ERROR- fseek /home/guilherme/simnibs_misc/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335 failed.error code 255 " It seems like there is an error within meshfix. In a prior thread on this mailing list ( https://mailman.drcmr.dk/pipermail/simnibs-discuss/2020-May/000051.html) this issue was raised and it wasn't clear if there was a resolution. I have looked at the subcortical_FS.stl file and it looks like how I would expect in a mesh viewer. I am running these commands on a T5810 workstation with Ubuntu 20.04 installed. Is there any solution to this issue? Thanks, Tayeb Zaidi -------------- next part -------------- An HTML attachment was scrubbed... URL: From oulap at drcmr.dk Thu Apr 29 13:40:57 2021 From: oulap at drcmr.dk (Oula) Date: Thu, 29 Apr 2021 13:40:57 +0200 Subject: [Simnibs-discuss] Meshfix error in SimNIBS-3.2.3 In-Reply-To: References: Message-ID: <20210429114843.DCA074AA958@curie.drcmr.dk> Hi Tayeb, Which version of FreeSurfer are you using? Due to a change in surface data formats, mri2mesh does not support FS versions >= 7.0 Best, Oula L?hett?j?: Tayeb Zaidi L?hetetty: 29. april 2021 09:10 Vastaanottaja: discuss at simnibs.org Aihe: [Simnibs-discuss] Meshfix error in SimNIBS-3.2.3 Hello, ??? I've been working to use SimNIBS-3.2 to generate head segmentation for several subjects from the Human Connectome Project. When running "mri2mesh --all subjectnumber T1w.nii T2w.nii" I successfully finish recon-all from Freesurfer and then the mri2mesh script raises an error when creating the subcortical mask. The exact error is: " mris_convert ./opticrad_FS.fsmesh ./opticrad_FS.stl /home/awarru/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix subcortical_FS.stl -a 2.0 --remove-handles -q -o subcortical.off ERROR- fseek /home/guilherme/simnibs_misc/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335 failed.error code 255 " It seems like there is an error within meshfix.? In a prior thread on this mailing list (https://mailman.drcmr.dk/pipermail/simnibs-discuss/2020-May/000051.html) this issue was raised and it wasn't clear if there was a resolution. I have looked at the subcortical_FS.stl file and it looks like how I would expect in a mesh viewer. I am running these commands on a T5810 workstation with Ubuntu 20.04 installed. Is there any solution to this issue? Thanks, Tayeb Zaidi -------------- next part -------------- An HTML attachment was scrubbed... URL: From tayebzaidi at gmail.com Thu Apr 29 15:08:13 2021 From: tayebzaidi at gmail.com (Tayeb Zaidi) Date: Thu, 29 Apr 2021 09:08:13 -0400 Subject: [Simnibs-discuss] Meshfix error in SimNIBS-3.2.3 In-Reply-To: <608a9d17.1c69fb81.f714e.e187SMTPIN_ADDED_MISSING@mx.google.com> References: <608a9d17.1c69fb81.f714e.e187SMTPIN_ADDED_MISSING@mx.google.com> Message-ID: Hi Oula, I just checked and am using FreeSurfer 7.1.1 -- I didn't know that mri2mesh doesn't support Freesurfer 7 and greater. Is this information in the mri2mesh documentation? Either way, thanks for your help! I'll install FreeSurfer 6 for now and retry. Regards, Tayeb On Thu, Apr 29, 2021 at 7:48 AM Oula wrote: > Hi Tayeb, > > > > Which version of FreeSurfer are you using? Due to a change in surface data > formats, mri2mesh does not support FS versions >= 7.0 > > > > Best, > > Oula > > > > *L?hett?j?: *Tayeb Zaidi > *L?hetetty: *29. april 2021 09:10 > *Vastaanottaja: *discuss at simnibs.org > *Aihe: *[Simnibs-discuss] Meshfix error in SimNIBS-3.2.3 > > > > Hello, > > > > I've been working to use SimNIBS-3.2 to generate head segmentation for > several subjects from the Human Connectome Project. When running "mri2mesh > --all subjectnumber T1w.nii T2w.nii" I successfully finish recon-all from > Freesurfer and then the mri2mesh script raises an error when creating the > subcortical mask. The exact error is: > > " > > mris_convert ./opticrad_FS.fsmesh ./opticrad_FS.stl > > /home/awarru/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix > subcortical_FS.stl -a 2.0 --remove-handles -q -o subcortical.off > > ERROR- fseek > /home/guilherme/simnibs_misc/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335 > failed.error code 255 > > " > > > > It seems like there is an error within meshfix. In a prior thread on this > mailing list ( > https://mailman.drcmr.dk/pipermail/simnibs-discuss/2020-May/000051.html) > this issue was raised and it wasn't clear if there was a resolution. I have > looked at the subcortical_FS.stl file and it looks like how I would expect > in a mesh viewer. > > I am running these commands on a T5810 workstation with Ubuntu 20.04 > installed. > > Is there any solution to this issue? > > > > Thanks, > > Tayeb Zaidi > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: