From vincent.rochas at fcbg.ch Mon Dec 5 12:11:35 2022 From: vincent.rochas at fcbg.ch (Vincent Rochas) Date: Mon, 5 Dec 2022 11:11:35 +0000 Subject: [Simnibs-discuss] charm head modelling problems Message-ID: Dear simNIBS users and programmers I have used simNIBS previous versions with very good results and reasonable simulations for tCS. I was using headreco function with two MRIs T1 and T2, converted from Dicom to Nifti using SPM12. I am now trying the new version of simNIBS (4.0) using the charm function and experiencing some troubles. - The MRIs I was previously using are apparently not compliant with the needed standard in term of orientation (?) and there was a complain about sform and qform annotation, so I was advised to use ?forceqform by the charm function which I did. - After using the ?forceqform option it runs the segmentation. However the resulting .msh file in the m2m folder corresponds to another face and head than my patient MRI! I tried to re-run the ernie segmentation (without needing the ?forceqform option). The command line was like: charm ernie ernie_T1.nii.gz ernie_T2.nii.gz The results is again this same face wrapped on ernie?s shape I guess. Or Ernie?s head wrapped differently I don?t know. In the case of the patient it is surely not the head and face of the patient at all, and this same head though. Also the segmentation of the cortex doesn?t look very precise, sulci are not well delineated. I then checked the log.html and I noticed a difference with the examples provided by simNIBS (the prototypic ernie segmentation). On the DEBUG line I have 'init_type': 'atlas' instead of 'init_type': mni' in the example segmentation. I don?t know if it is the problem but might explain why it is differently sticking the atlas maybe on the patient?s T1 as a result. That might be a trivial problem or an option that I missed. I would be happy to have your opinion. Best, Vincent -------------- next part -------------- An HTML attachment was scrubbed... URL: From oulap at drcmr.dk Mon Dec 5 12:58:06 2022 From: oulap at drcmr.dk (Oula Puonti) Date: Mon, 5 Dec 2022 12:58:06 +0100 Subject: [Simnibs-discuss] charm head modelling problems In-Reply-To: References: Message-ID: Hi Vincent, Could you maybe send the charm_report.html file to: support at simnibs.org Happy to look at the data as well if you're allowed to share it. Best, Oula On 12/5/22 12:11, Vincent Rochas wrote: > > Dear simNIBS users and programmers > > I have used simNIBS previous versions with very good results and > reasonable simulations for tCS. I was using /headreco/ function with > two MRIs T1 and T2, converted from Dicom to Nifti using SPM12. > > I am now trying the new version of simNIBS (4.0) using the /charm/ > function and experiencing some troubles. > - The MRIs I was previously using are apparently not compliant with > the needed standard in term of orientation (?) and there was a > complain about sform and qform annotation, so I was advised to use > ?forceqform by the /charm/ function which I did. > > - After using the ?forceqform option it runs the segmentation. However > the resulting .msh file in the m2m folder corresponds to another face > and head than my patient MRI! > > I tried to re-run the ernie segmentation (without needing the > ?forceqform option). The command line was like: charm ernie > ernie_T1.nii.gz ernie_T2.nii.gz The results is again this same face > wrapped on ernie?s shape I guess. Or Ernie?s head wrapped differently > I don?t know. In the case of the patient it is surely not the head and > face of the patient at all, and this same head though. Also the > segmentation of the cortex doesn?t look very precise, sulci are not > well delineated. > > I then checked the log.html and I noticed a difference with the > examples provided by simNIBS (the prototypic ernie segmentation). On > the DEBUG line I have 'init_type': 'atlas' instead of 'init_type': > mni' in the example segmentation. > > I don?t know if it is the problem but might explain why it is > differently sticking the atlas maybe on the patient?s T1 as a result. > > That might be a trivial problem or an option that I missed. I would be > happy to have your opinion. > > > Best, > > Vincent > > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -------------- next part -------------- An HTML attachment was scrubbed... URL: From MNAZAROVA at PARTNERS.ORG Fri Dec 9 03:40:54 2022 From: MNAZAROVA at PARTNERS.ORG (Nazarova, Mariia) Date: Fri, 9 Dec 2022 02:40:54 +0000 Subject: [Simnibs-discuss] error while using charm (instead of headreco) Message-ID: Dear colleagues, I`m sorry for bothering! I was really excited about the release of the new segmentation algorithm and tried to use charm for the first time. Then I have the following error (attached). I`m quite an inexperienced Linux user, may you please help me to solve it? Thank you so much in advance! Best, Maria The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Charm_error1 Type: application/octet-stream Size: 24146 bytes Desc: Charm_error1 URL: From jot.sheng at outlook.com Mon Dec 12 14:47:18 2022 From: jot.sheng at outlook.com (Sheng Yihong) Date: Mon, 12 Dec 2022 13:47:18 +0000 Subject: [Simnibs-discuss] questions about the seg_type Message-ID: Dear SimNIBS When I try to follow the tutorial to get a Leadfield on SimNIBS 4.0 TDCS optimization, I got a OSError. OSError: Could not find surface files in m2m folder. SPM-only segmentation? After I check the transformation.py I find the problem caused by segmentation type. But in the changelog4.0 Headreco and mri2mesh are deprecated. So I have no idea to solve the OSError. Could you help me to figure my problem out? Best wishes Yihong -------------- next part -------------- An HTML attachment was scrubbed... URL: From margaret.mcallister at duke.edu Tue Dec 13 00:24:53 2022 From: margaret.mcallister at duke.edu (Mags McAllister) Date: Mon, 12 Dec 2022 23:24:53 +0000 Subject: [Simnibs-discuss] Installing SimNIBS on Mac Message-ID: Hi, I previously installed SimNIBS on my Mac desktop without issue. I recently uninstalled it because I wanted to update to version 4.0.0. When I select the installer I am directed to a ?503 service unavailable? page. I?ve included the link that leads me to this page below. https://simnibs.github.io/simnibs/build/html/installation/simnibs_installer.html# Is this an issue with the website, installer, or my device? Thanks! Mags M. -------------- next part -------------- An HTML attachment was scrubbed... URL: From fidel.vilarodriguez at ubc.ca Tue Dec 13 07:22:07 2022 From: fidel.vilarodriguez at ubc.ca (Vila-Rodriguez, Fidel) Date: Tue, 13 Dec 2022 06:22:07 +0000 Subject: [Simnibs-discuss] Testing SIMNIBS 4.0 Message-ID: <112A5E9E-2E88-479D-8746-C1621985492A@mail.ubc.ca> Hi, I?m testing SIMNIBS 4.0 in a handful of subjects, and in all of them I get the same type of error (terminal console capture below) that I cannot see on the charm_log.htlm report (one attached here for reference) Any insights would be much appreciated. Thanks and best regards, Fidel Incorrect guard value: 4586839698203395468 python(66712,0x30989c000) malloc: *** set a breakpoint in malloc_error_break to debug python(66712,0x30958a000) malloc: Heap corruption detected, free list is damaged at 0x6000001e3f00 *** Incorrect guard value: 0 python(66712,0x30958a000) malloc: *** set a breakpoint in malloc_error_break to debug /Users/mandelbrot/Applications/SimNIBS-4.0/bin/charm: line 2: 66712 Abort trap: 6 "/Users/mandelbrot/Applications/SimNIBS-4.0/simnibs_env/bin/python" -E -u "/Users/mandelbrot/Applications/SimNIBS-4.0/simnibs_env/lib/python3.9/site-packages/simnibs/cli/charm.py -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.l.van.haren at umcg.nl Wed Dec 14 16:22:17 2022 From: s.l.van.haren at umcg.nl (Haren, SL van (cso)) Date: Wed, 14 Dec 2022 15:22:17 +0000 Subject: [Simnibs-discuss] Looking for literature Message-ID: Hi all, I am having a hard time looking for literature looking comparing the accuracy of finding the motor cortex in SimNIBS against the motor cortex found by n-TMS, (comparing the model against the real world). Does anyone have a idea which research might by useful for answering this question? Kind regards Stefan ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From asif08 at gmail.com Mon Dec 19 19:33:48 2022 From: asif08 at gmail.com (Asif Jamil) Date: Mon, 19 Dec 2022 13:33:48 -0500 Subject: [Simnibs-discuss] simnibs 4: numpy singular matrix error Message-ID: Hello- I?m using simnibs 4 to perform tDCS e-field simulation, and part of the pipeline is to calculate the E-field normal component on the fsaverage surface. For most of my subjects, the pipeline runs fine, however for one participant, I?m getting the following error: [ simnibs ]INFO: Interpolating to the middle of Gray Matter [ simnibs ]CRITICAL: Uncaught exception numpy.linalg.LinAlgError: Singular matrix Seems like this issue is related to there being a singular matrix. Is there a quick workaround to this error? Thanks Asif -------------- next part -------------- An HTML attachment was scrubbed... URL: From chivihuertasp at gmail.com Mon Dec 19 11:59:01 2022 From: chivihuertasp at gmail.com (Silvana Huertas) Date: Mon, 19 Dec 2022 11:59:01 +0100 Subject: [Simnibs-discuss] ROI analysis Message-ID: Hi, I have been trying to do a ROI analysis using surface, as in your page https://simnibs.github.io/simnibs/build/html/tutorial/analysis.html. I copied your example and changed the mesh to mine. I interpolated my mesh to the surface, using map_to_surface when I run the simulation. However, when I try to do the ROI analysis, I get an error in the line head_mesh.node_data{end}.name = region_name. The error says that we can't find the lh.4 region. I do not understand why this error happens. Could you help me, please? Below you can see my code sub=fullfile(foldersPath(time).folder,foldersPath(time).name,'mni_icbm152_t1_tal_TDCS_1_scalar.msh'); head_mesh = mesh_load_gmsh4(sub); pwd='C:\Users\Workspace-user\Documents\...\mni_icbm152_nlin_sym_09a'; [labels, snames] = subject_atlas(head_mesh, fullfile(pwd, 'm2m_mni_icbm152_t1_tal\'), 'HCP_MMP1'); region_name = 'lh.4'; roi_idx=find(strcmpi(snames, region_name)); node_idx = labels.node_data{end}.data==roi_idx; % Plot the ROI head_mesh.node_data{end+1}.data = int8(node_idx); head_mesh.node_data{end}.name = region_name; mesh_show_surface(head_mesh, 'field_idx', region_name) Thank you for your help, -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Tue Dec 20 10:49:02 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Tue, 20 Dec 2022 10:49:02 +0100 Subject: [Simnibs-discuss] Installing SimNIBS on Mac In-Reply-To: References: Message-ID: Hi Mags, there was a problem with the website. Please try again, it should work now. Best regards, Axel On 13-12-2022 00:24, Mags McAllister wrote: > > Hi, > > I previously installed SimNIBS on my Mac desktop without issue. I > recently uninstalled it because I wanted to update to version 4.0.0. > When I select the installer > > I am directed to a ?503 service unavailable? page. I?ve included the > link that leads me to this page below. > > https://simnibs.github.io/simnibs/build/html/installation/simnibs_installer.html# > > Is this an issue with the website, installer, or my device? > > Thanks! > > Mags M. > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -- Dr. Axel Thielscher Professor of Neurophysics and Neuroimaging 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: From axelt at drcmr.dk Tue Dec 20 11:10:43 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Tue, 20 Dec 2022 11:10:43 +0100 Subject: [Simnibs-discuss] questions about the seg_type In-Reply-To: References: Message-ID: <1302b981-747d-9e78-b1b9-1625876d5634@drcmr.dk> Dear Yihong, this error only exists in older simnibs versions prior to version 4. Please make sure you have the latest version installed, and that the paths are set to the latest version. You can test by opening a cmd or shell window and typing charm If that isn't found, please check your path settings. When you have head models created with simnibs 3 which you want to go on using, please use the command convert_3_to_4 before using these headmodels in simnibs 4. Best regards, Axel On 12-12-2022 14:47, Sheng Yihong wrote: > > Dear SimNIBS > > When I try to follow the tutorial to get a Leadfield on SimNIBS 4.0 > TDCS optimization, I got a OSError. > > *OSError*: Could not find surface files in m2m folder. SPM-only > segmentation? > > After I check the transformation.py I find the problem caused by > segmentation type. But in the changelog4.0 Headreco and mri2mesh are > deprecated. So I have no idea to solve the OSError. > > Could you help me to figure my problem out? > > Best wishes > > Yihong > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -- Dr. Axel Thielscher Professor of Neurophysics and Neuroimaging 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: From sfrandsen at bwh.harvard.edu Wed Dec 21 21:14:37 2022 From: sfrandsen at bwh.harvard.edu (Frandsen, Summer Brianne) Date: Wed, 21 Dec 2022 20:14:37 +0000 Subject: [Simnibs-discuss] Python Library Not Working Message-ID: Hello, I am trying to use some of the command line tools such as mni2subject_coords on a Mac Ventura OS, but it simply says that the command cannot be found. I have uninstalled and reinstalled the software, and tried various options. I have several colleagues with the same issues. Are there any other set-up steps needed for the command line tools to work? Or any typical trouble shooting tips? Thanks, Summer Frandsen The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Fri Dec 23 18:21:47 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Fri, 23 Dec 2022 18:21:47 +0100 Subject: [Simnibs-discuss] Python Library Not Working In-Reply-To: References: Message-ID: <08189835-e648-5951-4dc7-5951d89b12d5@drcmr.dk> Hi Summer, thanks for contacting us. There is a install.log file in the simnibs folder. Can you please send this to us? Furthermore, there should be a subfolder "bin" in the simnibs folder. Can you please check whether this subfolder exists and whether it contains the command line tools? Best regards, Axel On 21-12-2022 21:14, Frandsen, Summer Brianne wrote: > > Hello, > > I am trying to use some of the command line tools such as > mni2subject_coords on a Mac Ventura OS, but it simply says that the > command cannot be found. > > I have uninstalled and reinstalled the software, and tried various > options. I have several colleagues with the same issues. Are there any > other set-up steps needed for the command line tools to work? Or any > typical trouble shooting tips? > > Thanks, > > Summer Frandsen > > The information in this e-mail is intended only for the person to whom > it is addressed.? If you believe this e-mail was sent to you in error > and the e-mail contains patient information, please contact the Mass > General Brigham Compliance HelpLine at > https://www.massgeneralbrigham.org/complianceline . > > > Please note that this e-mail is not secure (encrypted).? If you do not > wish to continue communication over unencrypted e-mail, please notify > the sender of this message immediately.? Continuing to send or respond > to e-mail after receiving this message means you understand and accept > this risk and wish to continue to communicate over unencrypted e-mail. > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -- Dr. Axel Thielscher Professor of Neurophysics and Neuroimaging 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: From G.Lale at campus.lmu.de Fri Dec 30 15:13:12 2022 From: G.Lale at campus.lmu.de (=?utf-8?Q?G=C3=BClce_Lale?=) Date: Fri, 30 Dec 2022 15:13:12 +0100 Subject: [Simnibs-discuss] Problem with editing segmentation results Message-ID: <92497AD4-8741-4F27-977F-A1EE97810DFF@campus.lmu.de> Hello, I?ve been editing my segmentation results with Freeview following the instructions on this page: https://simnibs.github.io/simnibs/build/html/documentation/command_line/headreco.html My aim is to correct the CSF since it overflows to bone in some of the segmentations. After I edit the segmentation on the binary mask in the /mask_prep folder (in this case MASK_CSF.nii.gz), I run headreco surfacemesh and headreco volumemesh, the colors of the segmentation changes, these are saved in , SubID_final_contr.nii file. However, the lines saved in head_contr.fmesh and brain_contr.fmesh that define the boundary between bone and CSF are not changing. I tried to do these steps with CAT12 as well as without CAT12, with - -no -cat command. However, both of them resulted in the same way. Am I successfully editing the segmentation so that the magnetic field simulation done by SimNIBS will use the correct tissue borders? Or, do I have to apply something else in order to edit the line boundaries as well? Thank you for your help and answers in advance. Best wishes, G?lce G?lce Lale MSc Neurosciences -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrew.westbrook at brown.edu Sat Dec 31 12:20:51 2022 From: andrew.westbrook at brown.edu (Westbrook, Andrew) Date: Sat, 31 Dec 2022 06:20:51 -0500 Subject: [Simnibs-discuss] Issue with Export to Brainsight Message-ID: Hello, I am attempting to export my TMS Optimization results (estimated via the ADM method) to a Brainsight-readable .xml file, but I am getting the following error when I try to execute brainsight().write(opt_mat, fn) [ simnibs ]CRITICAL: Uncaught exception AssertionError: Expecting array with shape (4, 4, N instrument marker). As you can see in the attached python script, I am using a standard set of arguments to set up my optimization routine, so I don't know why the export function isn't working. Would you please help me address this issue? Note that the optimization itself appears to execute without error. Also, FWIW, I am running on Mac OS Big Sur 11.7, and I just installed my version of SimNIBS yesterday. Thank you, Andrew -- Andrew Westbrook Post-Doctoral Research Associate Department of Cognitive, Linguistics, and Psychological Sciences Brown University 190 Thayer Street Providence, RI 02912 Cell: +1-919-360-5399 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: expSimNIBStoBrainsight.py Type: text/x-python-script Size: 1207 bytes Desc: not available URL: