From axelt at drcmr.dk Wed Jun 2 14:50:18 2021 From: axelt at drcmr.dk (Axel Thielscher) Date: Wed, 2 Jun 2021 14:50:18 +0200 Subject: [Simnibs-discuss] SimNIBS simulation - TMS study - Overlap figure In-Reply-To: <2d3cb36871ba48bbb00cd88bda1218e6@UM-MAIL3217.unimaas.nl> References: <1621441760989.125@student.maastrichtuniversity.nl> <2d3cb36871ba48bbb00cd88bda1218e6@UM-MAIL3217.unimaas.nl> Message-ID: Hi, for determining an overlap, you will have to set a threshold to then show the regions where both TMS fields exceed this threshold.? In the attached example code , I've used 0.75 as threshold, please adjust this according to your needs. Regions where the first stimulation exceeds the threshold are coded as 1, regions where the second stimulation exceeds the threshold are coded as 2, the overlap is coded as 3. Best regards, Axel On 5/26/2021 2:33 PM, Dantas, A (MW) wrote: > > Dear all, > > My student Nancy ?bner got in touch with you recently about the need > for a Magventure double cone coil simulation using SimNIBS. > > We ran the simulations successfully, so first of all I would like to > thank you! > > We have an experiment deactivating the VMPFC vs. deactivating the > right DLPFC. So far, we managed to run both simulations, but it would > be great if we could the overlap image of stimulating these two areas. > We tried to make it but did not succeed. > > Do you think you could help me to build that? > > Thank you! > > Kind regards, > > Aline Dantas > > > _______________________________________________ > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: ojeaodfgjimjdmnp.png Type: image/png Size: 661752 bytes Desc: not available URL: -------------- next part -------------- fn_msh1 = 'ernie_TMS_1-0001_MagVenture_MC_B70_scalar.msh'; fn_msh2 = 'ernie_TMS_1-0002_MagVenture_MC_B70_scalar.msh'; fn_out = 'overlap.msh'; threshold = 0.75; % in [V/m] % load simulation results m1 = mesh_load_gmsh4(fn_msh1); m2 = mesh_load_gmsh4(fn_msh2); % find elements where the field strength exceeds the threshold idx_tri_1 = m1.element_data{ get_field_idx(m1,'normE','elem') }.tridata >= threshold; idx_tet_1 = m1.element_data{ get_field_idx(m1,'normE','elem') }.tetdata >= threshold; idx_tri_2 = m2.element_data{ get_field_idx(m2,'normE','elem') }.tridata >= threshold; idx_tet_2 = m2.element_data{ get_field_idx(m2,'normE','elem') }.tetdata >= threshold; % make a new mesh to show overlap m_new = m1; m_new.element_data={}; m_new.element_data{1}.name = 'overlap'; m_new.element_data{1}.tridata = double(idx_tri_1); m_new.element_data{1}.tetdata = double(idx_tet_1); m_new.element_data{1}.tridata(idx_tri_2) = 2; m_new.element_data{1}.tetdata(idx_tet_2) = 2; m_new.element_data{1}.tridata(idx_tri_1&idx_tri_2) = 3; m_new.element_data{1}.tetdata(idx_tet_1&idx_tet_2) = 3; mesh_save_gmsh4(m_new, fn_out); mesh_show_surface(m_new,'field_idx','overlap') From a.dantas at maastrichtuniversity.nl Wed Jun 2 15:10:09 2021 From: a.dantas at maastrichtuniversity.nl (Dantas, A (MW)) Date: Wed, 2 Jun 2021 13:10:09 +0000 Subject: [Simnibs-discuss] SimNIBS simulation - TMS study - Overlap figure In-Reply-To: References: <1621441760989.125@student.maastrichtuniversity.nl> <2d3cb36871ba48bbb00cd88bda1218e6@UM-MAIL3217.unimaas.nl> Message-ID: Thank you very much! I?ll try this solution. Kind regards, Aline Dantas From: Axel Thielscher Sent: Wednesday, 2 June 2021 14:50 To: Dantas, A (MW) ; discuss at simnibs.org; jonas.persson at neuro.uu.se Cc: ?bner, Nancy (Stud. FHML / Alumni UCV) Subject: Re: [Simnibs-discuss] SimNIBS simulation - TMS study - Overlap figure Hi, for determining an overlap, you will have to set a threshold to then show the regions where both TMS fields exceed this threshold. In the attached example code , I've used 0.75 as threshold, please adjust this according to your needs. Regions where the first stimulation exceeds the threshold are coded as 1, regions where the second stimulation exceeds the threshold are coded as 2, the overlap is coded as 3. [cid:image001.png at 01D757C1.60011FB0] Best regards, Axel On 5/26/2021 2:33 PM, Dantas, A (MW) wrote: Dear all, My student Nancy ?bner got in touch with you recently about the need for a Magventure double cone coil simulation using SimNIBS. We ran the simulations successfully, so first of all I would like to thank you! We have an experiment deactivating the VMPFC vs. deactivating the right DLPFC. So far, we managed to run both simulations, but it would be great if we could the overlap image of stimulating these two areas. We tried to make it but did not succeed. Do you think you could help me to build that? Thank you! Kind regards, Aline Dantas _______________________________________________ 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 661752 bytes Desc: image001.png URL: From colin.mcnabb at utah.edu Fri Jun 4 22:11:47 2021 From: colin.mcnabb at utah.edu (COLIN LEE MCNABB) Date: Fri, 4 Jun 2021 20:11:47 +0000 Subject: [Simnibs-discuss] Error With Meshfix Message-ID: <27D9F9B4-4E96-4711-B6AB-7E8D5C6CD8BC@utah.edu> Hello, I am an undergraduate student at the University of Utah, and I am attempting to build a head model from macaque brain MRI imaging. I am running my project on the HPC resources here; the input is meshfix rh.gm.stl -o gm_fixed2.off The output given almost immediately is meshfix rh.gm.stl ERROR- fseek /home/guilherme/simnibs_misc/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335 failed. I saw a similar issue online (https://mailman.drcmr.dk/pipermail/simnibs-discuss/2020-May/000052.html) and was wondering if there was a known fix. Please let me know if you need any additional information from me. Thank you. - Colin -------------- next part -------------- An HTML attachment was scrubbed... URL: From kristofferm at drcmr.dk Mon Jun 7 09:14:02 2021 From: kristofferm at drcmr.dk (Kristoffer Madsen) Date: Mon, 7 Jun 2021 09:14:02 +0200 Subject: [Simnibs-discuss] Error With Meshfix In-Reply-To: <27D9F9B4-4E96-4711-B6AB-7E8D5C6CD8BC@utah.edu> References: <27D9F9B4-4E96-4711-B6AB-7E8D5C6CD8BC@utah.edu> Message-ID: It could be related to the internal format of the stl file, but hard to say without having the file. You could try to convert it to a ASCII based stl with another program and see if that fixes the problem, it would good if you could let us know if it worked. Otherwise it might also be an option to provide us with the stl file if you are allowed to share it. Best, Kristoffer On Mon, 7 Jun 2021 at 08:57, COLIN LEE MCNABB wrote: > > Hello, > > I am an undergraduate student at the University of Utah, and I am attempting to build a head model from macaque brain MRI imaging. I am running my project on the HPC resources here; the input is > > meshfix rh.gm.stl -o gm_fixed2.off > > The output given almost immediately is > > meshfix rh.gm.stl > > ERROR- fseek /home/guilherme/simnibs_misc/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335 failed. > > I saw a similar issue online (https://mailman.drcmr.dk/pipermail/simnibs-discuss/2020-May/000052.html) and was wondering if there was a known fix. > Please let me know if you need any additional information from me. > Thank you. > > - Colin > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss From s.beumer at tue.nl Tue Jun 8 12:38:17 2021 From: s.beumer at tue.nl (Beumer, Steven) Date: Tue, 8 Jun 2021 10:38:17 +0000 Subject: [Simnibs-discuss] Normal component E-field in Matlab after optimization Message-ID: Dear SimNibs team, I am writing a little MATLAB app to do optimizations in SimNibs via a GUI, which is going very well. In the GUI I would like to plot the fields and the histogram, which I do via the standard data reading scripts, however I have troubles getting the normal component of the E-field. I tried giving the optimization structure a map_to_surf = true attribute, which does not work. Is there a way to get the normal component without doing the simulation afterwards with the optimized electrodes? Kind regards and a lot of thanks in advance, Steven Beumer PhD student at the Eindhoven University of Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: From fangc at drcmr.dk Wed Jun 9 10:56:55 2021 From: fangc at drcmr.dk (fangc) Date: Wed, 09 Jun 2021 10:56:55 +0200 Subject: [Simnibs-discuss] Normal component E-field in Matlab after optimization In-Reply-To: References: Message-ID: <982ec23d7e097361c798a1e266f890b4@drcmr.dk> Dear Steven, The attribute 'map_to_surf' will map your results to the gray matter central surface and not give you the normal component of the E field. What you want to do might be a little post-processing. I do not know which language you use for your development, but in python you can simply do the following, for example, if you have a mesh in FsAverage space: field_name = 'E_normal' results_fsavg.field[field_name].value You can find more details here: https://simnibs.github.io/simnibs/build/html/tutorial/advanced/group_analysis.html?highlight=normal It also has a Matlab example for the same purpose. Good luck. And please let us know if you have further questions. Best, Fang On 2021-06-08 12:38, Beumer, Steven wrote: > Dear SimNibs team, > > I am writing a little MATLAB app to do optimizations in SimNibs via a > GUI, which is going very well. > > In the GUI I would like to plot the fields and the histogram, which I > do via the standard data reading scripts, however I have troubles > getting the normal component of the E-field. > > I tried giving the optimization structure a map_to_surf = true > attribute, which does not work. Is there a way to get the normal > component without doing the simulation afterwards with the optimized > electrodes? > > Kind regards and a lot of thanks in advance, > > Steven Beumer > > PhD student at the Eindhoven University of Technology > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss From s.beumer at tue.nl Wed Jun 9 12:58:01 2021 From: s.beumer at tue.nl (Beumer, Steven) Date: Wed, 9 Jun 2021 10:58:01 +0000 Subject: [Simnibs-discuss] Normal component E-field in Matlab after optimization In-Reply-To: <982ec23d7e097361c798a1e266f890b4@drcmr.dk> References: <982ec23d7e097361c798a1e266f890b4@drcmr.dk> Message-ID: Dear Fang and the SimNibs team, . Thank you for your answer, I understand the error in my reasoning indeed with map_to_surf, I use Matlab for my development and I would like to have my mesh in FsAverage indeed. The problem that I have though is that I would like to have this after an optimization call, which also returns the fields, instead of after a tDCS simulation. Using the following does not yield the mapped fields (probably because opt_struct doesn't have those options) : S = opt_struct('TDCSoptimize'); S.map_to_fsavg = true; S.map_to_mni = true; A workaround would be to simulate the optimized structure with the flags put to true, however I was curious if there would be a more elegant solution to this. Is there a solution for this or should I go for the workaround? Kind regards and many thanks for your help, Steven -----Original Message----- From: fangc Sent: Wednesday, June 9, 2021 10:57 AM To: Beumer, Steven Cc: simnibs-discuss at drcmr.dk Subject: Re: [Simnibs-discuss] Normal component E-field in Matlab after optimization Dear Steven, The attribute 'map_to_surf' will map your results to the gray matter central surface and not give you the normal component of the E field. What you want to do might be a little post-processing. I do not know which language you use for your development, but in python you can simply do the following, for example, if you have a mesh in FsAverage space: field_name = 'E_normal' results_fsavg.field[field_name].value You can find more details here: https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsimnibs.github.io%2Fsimnibs%2Fbuild%2Fhtml%2Ftutorial%2Fadvanced%2Fgroup_analysis.html%3Fhighlight%3Dnormal&data=04%7C01%7C%7Cd72f4185a1954759b71208d92b2488d8%7Ccc7df24760ce4a0f9d75704cf60efc64%7C1%7C1%7C637588258179721089%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=eYAXvGd%2FbxSvJnXoIoBUbF6IHgv1fVQR%2FmBiY9HoQDk%3D&reserved=0 It also has a Matlab example for the same purpose. Good luck. And please let us know if you have further questions. Best, Fang On 2021-06-08 12:38, Beumer, Steven wrote: > Dear SimNibs team, > > I am writing a little MATLAB app to do optimizations in SimNibs via a > GUI, which is going very well. > > In the GUI I would like to plot the fields and the histogram, which I > do via the standard data reading scripts, however I have troubles > getting the normal component of the E-field. > > I tried giving the optimization structure a map_to_surf = true > attribute, which does not work. Is there a way to get the normal > component without doing the simulation afterwards with the optimized > electrodes? > > Kind regards and a lot of thanks in advance, > > Steven Beumer > > PhD student at the Eindhoven University of Technology > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.drcmr.dk%2Fmailman%2Flistinfo%2Fsimnibs-discuss&data=04%7C01%7C%7Cd72f4185a1954759b71208d92b2488d8%7Ccc7df24760ce4a0f9d75704cf60efc64%7C1%7C1%7C637588258179731041%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=%2FtZczCRJ8UU0sOp3cZdRWr8jzhiJIX%2BZkGm3SqLXe8k%3D&reserved=0 From a.dantas at maastrichtuniversity.nl Thu Jun 10 11:58:41 2021 From: a.dantas at maastrichtuniversity.nl (Dantas, A (MW)) Date: Thu, 10 Jun 2021 09:58:41 +0000 Subject: [Simnibs-discuss] SimNIBS simulation - TMS study - Overlap figure In-Reply-To: References: <1621441760989.125@student.maastrichtuniversity.nl> <2d3cb36871ba48bbb00cd88bda1218e6@UM-MAIL3217.unimaas.nl> Message-ID: <700968ed497541309526b52395e0a60e@UM-MAIL3217.unimaas.nl> Dear Axel, One more question: What about the stimulation intensities? Can we adjust the intensity to check if the overlap is influenced by it? Kind regards, Aline Dantas PhD candidate Human Decision and Policy Design Departments of Marketing and Supply Chain Management (SBE) and Cognitive Neurosciences (FPN) Room F2.02. Tongersestraat 53, 6211 LM Room 2.018. Oxfordlaan 55, 6229 EV From: Dantas, A (MW) Sent: Wednesday, 2 June 2021 15:10 To: 'Axel Thielscher' ; discuss at simnibs.org; jonas.persson at neuro.uu.se Cc: ?bner, Nancy (Stud. FHML / Alumni UCV) Subject: RE: [Simnibs-discuss] SimNIBS simulation - TMS study - Overlap figure Thank you very much! I?ll try this solution. Kind regards, Aline Dantas From: Axel Thielscher > Sent: Wednesday, 2 June 2021 14:50 To: Dantas, A (MW) >; discuss at simnibs.org; jonas.persson at neuro.uu.se Cc: ?bner, Nancy (Stud. FHML / Alumni UCV) > Subject: Re: [Simnibs-discuss] SimNIBS simulation - TMS study - Overlap figure Hi, for determining an overlap, you will have to set a threshold to then show the regions where both TMS fields exceed this threshold. In the attached example code , I've used 0.75 as threshold, please adjust this according to your needs. Regions where the first stimulation exceeds the threshold are coded as 1, regions where the second stimulation exceeds the threshold are coded as 2, the overlap is coded as 3. [cid:image001.png at 01D75DEF.F4C11360] Best regards, Axel On 5/26/2021 2:33 PM, Dantas, A (MW) wrote: Dear all, My student Nancy ?bner got in touch with you recently about the need for a Magventure double cone coil simulation using SimNIBS. We ran the simulations successfully, so first of all I would like to thank you! We have an experiment deactivating the VMPFC vs. deactivating the right DLPFC. So far, we managed to run both simulations, but it would be great if we could the overlap image of stimulating these two areas. We tried to make it but did not succeed. Do you think you could help me to build that? Thank you! Kind regards, Aline Dantas _______________________________________________ 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 661752 bytes Desc: image001.png URL: From fangc at drcmr.dk Wed Jun 16 11:31:32 2021 From: fangc at drcmr.dk (fangc) Date: Wed, 16 Jun 2021 11:31:32 +0200 Subject: [Simnibs-discuss] Normal component E-field in Matlab after optimization In-Reply-To: References: <982ec23d7e097361c798a1e266f890b4@drcmr.dk> Message-ID: Dear Steven, You will need to run the simulation again. SimNIBS aims to facilitate the use of individualized stimulation modeling, which leads to the fact that the Leadfield is calculated at an individual subject level, not on the standard spaces, such as FreeSurfer?s FsAverage. So you could simply rerun the simulation to get the fields. Hope it helps. Kind regards, Fang On 2021-06-09 12:58, Beumer, Steven wrote: > Dear Fang and the SimNibs team, > . > Thank you for your answer, I understand the error in my reasoning > indeed with map_to_surf, I use Matlab for my development and I would > like to have my mesh in FsAverage indeed. The problem that I have > though is that I would like to have this after an optimization call, > which also returns the fields, instead of after a tDCS simulation. > > Using the following does not yield the mapped fields (probably because > opt_struct doesn't have those options) : > S = opt_struct('TDCSoptimize'); > S.map_to_fsavg = true; > S.map_to_mni = true; > > A workaround would be to simulate the optimized structure with the > flags put to true, however I was curious if there would be a more > elegant solution to this. > Is there a solution for this or should I go for the workaround? > > Kind regards and many thanks for your help, > Steven > > -----Original Message----- > From: fangc > Sent: Wednesday, June 9, 2021 10:57 AM > To: Beumer, Steven > Cc: simnibs-discuss at drcmr.dk > Subject: Re: [Simnibs-discuss] Normal component E-field in Matlab > after optimization > > Dear Steven, > > The attribute 'map_to_surf' will map your results to the gray matter > central surface and not give you the normal component of the E field. > What you want to do might be a little post-processing. I do not know > which language you use for your development, but in python you can > simply do the following, for example, if you have a mesh in FsAverage > space: > > field_name = 'E_normal' > results_fsavg.field[field_name].value > > You can find more details here: > https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsimnibs.github.io%2Fsimnibs%2Fbuild%2Fhtml%2Ftutorial%2Fadvanced%2Fgroup_analysis.html%3Fhighlight%3Dnormal&data=04%7C01%7C%7Cd72f4185a1954759b71208d92b2488d8%7Ccc7df24760ce4a0f9d75704cf60efc64%7C1%7C1%7C637588258179721089%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=eYAXvGd%2FbxSvJnXoIoBUbF6IHgv1fVQR%2FmBiY9HoQDk%3D&reserved=0 > > It also has a Matlab example for the same purpose. Good luck. And > please let us know if you have further questions. > > Best, > Fang > > On 2021-06-08 12:38, Beumer, Steven wrote: >> Dear SimNibs team, >> >> I am writing a little MATLAB app to do optimizations in SimNibs via a >> GUI, which is going very well. >> >> In the GUI I would like to plot the fields and the histogram, which I >> do via the standard data reading scripts, however I have troubles >> getting the normal component of the E-field. >> >> I tried giving the optimization structure a map_to_surf = true >> attribute, which does not work. Is there a way to get the normal >> component without doing the simulation afterwards with the optimized >> electrodes? >> >> Kind regards and a lot of thanks in advance, >> >> Steven Beumer >> >> PhD student at the Eindhoven University of Technology >> _______________________________________________ >> Simnibs-discuss mailing list >> Simnibs-discuss at drcmr.dk >> https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.drcmr.dk%2Fmailman%2Flistinfo%2Fsimnibs-discuss&data=04%7C01%7C%7Cd72f4185a1954759b71208d92b2488d8%7Ccc7df24760ce4a0f9d75704cf60efc64%7C1%7C1%7C637588258179731041%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=%2FtZczCRJ8UU0sOp3cZdRWr8jzhiJIX%2BZkGm3SqLXe8k%3D&reserved=0 > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss From miran045 at umn.edu Fri Jun 18 21:16:23 2021 From: miran045 at umn.edu (Oscar Miranda-Dominguez) Date: Fri, 18 Jun 2021 14:16:23 -0500 Subject: [Simnibs-discuss] Problems downloading simnibs Message-ID: Hi I am trying to download simnibs but I got the following message: Proxy Error The proxy server received an invalid response from an upstream server. The proxy server could not handle the request *GET /userregistration2 *. Reason: *Error reading from remote server* Is the server down? Thank you and best regards Oscar Oscar Miranda-Dominguez, MSc, PhD Assistant Professor | Department of Pediatrics | Medical School University of Minnesota miran045 at umn.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From fang.cao at regionh.dk Mon Jun 21 11:41:21 2021 From: fang.cao at regionh.dk (Fang Cao) Date: Mon, 21 Jun 2021 09:41:21 +0000 Subject: [Simnibs-discuss] Problems downloading simnibs In-Reply-To: References: Message-ID: Dear Oscar, Could you let me know which webpage you are using for the downloading? We recommend you use: https://simnibs.drcmr.dk/userregistration2 If you succeeded to register your information, you will see the downloading page like this: [cid:c9c0a77a-59f0-4716-9b54-de8f5ae44b38] There you can choose which version you want to download according to your operating system. In fact, the files are on the public Github server, which is unlikely to crash. Otherwise, you may try another browser to download Simnibs. Please let us know if you have additional questions. Good luck! Kind regards, Fang ________________________________ From: Simnibs-discuss on behalf of Oscar Miranda-Dominguez Sent: Friday, 18 June 2021 21.16 To: discuss at simnibs.org Subject: [Simnibs-discuss] Problems downloading simnibs Hi I am trying to download simnibs but I got the following message: Proxy Error The proxy server received an invalid response from an upstream server. The proxy server could not handle the request GET /userregistration2. Reason: Error reading from remote server Is the server down? Thank you and best regards Oscar Oscar Miranda-Dominguez, MSc, PhD Assistant Professor | Department of Pediatrics | Medical School University of Minnesota miran045 at umn.edu ________________________________ Region Hovedstaden anvender de personoplysninger, du giver os i forbindelse med din henvendelse. Du kan laese mere om form?let med anvendelsen samt dine rettigheder p? vores hjemmeside: www.regionh.dk/persondatapolitik -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 69066 bytes Desc: image.png URL: From xc.teruel at gmail.com Mon Jun 21 13:06:03 2021 From: xc.teruel at gmail.com (xavier corominas) Date: Mon, 21 Jun 2021 13:06:03 +0200 Subject: [Simnibs-discuss] Cerebellum tDCS Message-ID: Good morning, delighted to meet you, My name is Xavier Corominas, I am a PhD student at the University Rovira i Virgili (Spain) under the direction of Dr. Maria Tresa Colomina (URV) and Dr. Antoni Valero (ICM-Paris). Since a few months ago I have started to work with computational simulation in SimNIBS and I have encountered a problem, that is why I am contacting you. I am trying to make an optimised setup of 2 targets (DLPC + anterior cerebellum) for a clinical trial of tDCS in stroke (note that we will use an 8-electrode device for stimulation). When running the simulation, the frontal target performs correctly but the cerebellar target disappears. The cerebellum disappears in the Gmsh file and the target changes coordinates and is represented on the posterior parietal cortex (the area closest to the cerebellum). I would like to ask how I can solve this issue as it does not take into account the cerebellum and I do not know how I should proceed. Thank you in advance for all your attention. Cordially. Xavier Corominas Teruel -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Thu Jun 24 21:05:27 2021 From: axelt at drcmr.dk (Axel Thielscher) Date: Thu, 24 Jun 2021 21:05:27 +0200 Subject: [Simnibs-discuss] SimNIBS simulation - TMS study - Overlap figure In-Reply-To: <700968ed497541309526b52395e0a60e@UM-MAIL3217.unimaas.nl> References: <1621441760989.125@student.maastrichtuniversity.nl> <2d3cb36871ba48bbb00cd88bda1218e6@UM-MAIL3217.unimaas.nl> <700968ed497541309526b52395e0a60e@UM-MAIL3217.unimaas.nl> Message-ID: Hi, you could adjust the dI/dt when setting up the simulations to realistic values (the standard in the GUI is 1 A/mue_s, which is very low; values exceeding ~70 A/Mue_s would be realistic for standard coils). You will then also have to adjust the threshold in the script to a more realistic value for a e-field strength that would result in neural excitation. You can try ~60 V/m, for example. However, as long as the dI/dt of both simulations is the same, the outcome will be identical to that of the original script when selecting the threshold accordingly (as setting the dI/dt only linearly scales the simulated fields) - the selected threshold is somewhat arbitrary as the exact cortical excitation thresholds are not fully known and just determines how large the overlap region is. When you don't use the same stimulation intensity for both stimulations, then it would be for sure important to set the dI/dt values, as this will then also shift the position of the overlap region. Best regards, Axel On 6/10/2021 11:58 AM, Dantas, A (MW) wrote: > > Dear Axel, > > One more question: What about the stimulation intensities? Can we > adjust the intensity to check if the overlap is influenced by it? > > Kind regards, > > *Aline Dantas * > > /PhD candidate/ > > /Human Decision and Policy Design/ > > /Departments of Marketing and Supply Chain Management (SBE) and > Cognitive Neurosciences (FPN)/ > > Room F2.02. Tongersestraat 53, 6211 LM > > Room 2.018. Oxfordlaan 55, 6229 EV > > *From:*Dantas, A (MW) > *Sent:* Wednesday, 2 June 2021 15:10 > *To:* 'Axel Thielscher' ; discuss at simnibs.org; > jonas.persson at neuro.uu.se > *Cc:* ?bner, Nancy (Stud. FHML / Alumni UCV) > > *Subject:* RE: [Simnibs-discuss] SimNIBS simulation - TMS study - > Overlap figure > > Thank you very much! I?ll try this solution. > > Kind regards, > > Aline Dantas > > *From:*Axel Thielscher > > *Sent:* Wednesday, 2 June 2021 14:50 > *To:* Dantas, A (MW) >; discuss at simnibs.org > ; jonas.persson at neuro.uu.se > > *Cc:* ?bner, Nancy (Stud. FHML / Alumni UCV) > > > *Subject:* Re: [Simnibs-discuss] SimNIBS simulation - TMS study - > Overlap figure > > Hi, > > for determining an overlap, you will have to set a threshold to then > show the regions where both TMS fields exceed this threshold.? In the > attached example code , I've used 0.75 as threshold, please adjust > this according to your needs. > > Regions where the first stimulation exceeds the threshold are coded as > 1, regions where the second stimulation exceeds the threshold are > coded as 2, the overlap is coded as 3. > > Best regards, > > Axel > > On 5/26/2021 2:33 PM, Dantas, A (MW) wrote: > > Dear all, > > My student Nancy ?bner got in touch with you recently about the > need for a Magventure double cone coil simulation using SimNIBS. > > We ran the simulations successfully, so first of all I would like > to thank you! > > We have an experiment deactivating the VMPFC vs. deactivating the > right DLPFC. So far, we managed to run both simulations, but it > would be great if we could the overlap image of stimulating these > two areas. We tried to make it but did not succeed. > > Do you think you could help me to build that? > > Thank you! > > Kind regards, > > Aline Dantas > > _______________________________________________ > > 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/ -- 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 661752 bytes Desc: not available URL: From fabiola.alonso-orozco at inserm.fr Fri Jun 25 13:08:32 2021 From: fabiola.alonso-orozco at inserm.fr (Fabiola ALONSO OROZCO) Date: Fri, 25 Jun 2021 13:08:32 +0200 Subject: [Simnibs-discuss] headreco issue Message-ID: Hello , I'm trying to generate a head model in Windows 10. When using headreco I got the following error: OSError: Could not find tissue probability maps. Probably something went wrong with the Matlab call or SPM I saw that somebody else asked for this same error in the f?rum and he was suggested to install a newer versi?n. I just downloaded the last versi?n of SimNIBS (3.2) therefore this solution won't work for me. Do you have any clue to avoid this problem? Many thanks in advance, Fabiola Alonso Provenance : Courrier [1] pour Windows 10 Links: ------ [1] https://go.microsoft.com/fwlink/?LinkId=550986 -------------- next part -------------- An HTML attachment was scrubbed... URL: From fabiola.alonso-orozco at inserm.fr Mon Jun 28 11:21:14 2021 From: fabiola.alonso-orozco at inserm.fr (Fabiola ALONSO OROZCO) Date: Mon, 28 Jun 2021 11:21:14 +0200 Subject: [Simnibs-discuss] headreco issue In-Reply-To: References: Message-ID: <534c33ec7354278c8981f76372e73603@inserm.fr> Dear Fang, thank you for your reply! Please find attached the log file. Yes, I have a file called: T1fs_conform.nii By the way, I forgot to say that I've been using the example dataset provided, ernie. Thanks again and kind regards, Fabiola Le 2021-06-28 11:01, Fang Cao a ?crit : > Dear Fabiola, > > could you send us the log file? It is located in your output directory: > > m2m_/headreco_log.html > > And could you also check if you could find any file like > > m2m_/segment/spm/c*T1fs_conform* > > Kind regards, > Fang > > ------------------------- > > FROM: Simnibs-discuss on behalf of Fabiola ALONSO OROZCO > SENT: Friday, 25 June 2021 13.08 > TO: simnibs-discuss at drcmr.dk > SUBJECT: [Simnibs-discuss] headreco issue > > Hello , > > I'm trying to generate a head model in Windows 10. When using headreco I got the following error: > > OSError: Could not find tissue probability maps. > > Probably something went wrong with the Matlab call or SPM > > I saw that somebody else asked for this same error in the f?rum and he was suggested to install a newer versi?n. I just downloaded the last versi?n of SimNIBS (3.2) therefore this solution won't work for me. > > Do you have any clue to avoid this problem? > > Many thanks in advance, > > Fabiola Alonso > > Provenance : Courrier [1] pour Windows 10 > > ------------------------- > > Region Hovedstaden anvender de personoplysninger, du giver os i forbindelse med din henvendelse. Du kan l?se mere om form?let med anvendelsen samt dine rettigheder p? vores hjemmeside: www.regionh.dk/persondatapolitik Links: ------ [1] https://go.microsoft.com/fwlink/?LinkId=550986 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: headreco_log.html Type: text/troff Size: 1173623 bytes Desc: not available URL: From fang.cao at regionh.dk Mon Jun 28 11:01:41 2021 From: fang.cao at regionh.dk (Fang Cao) Date: Mon, 28 Jun 2021 09:01:41 +0000 Subject: [Simnibs-discuss] headreco issue In-Reply-To: References: Message-ID: Dear Fabiola, could you send us the log file? It is located in your output directory: m2m_/headreco_log.html And could you also check if you could find any file like m2m_/segment/spm/c*T1fs_conform* Kind regards, Fang ________________________________ From: Simnibs-discuss on behalf of Fabiola ALONSO OROZCO Sent: Friday, 25 June 2021 13.08 To: simnibs-discuss at drcmr.dk Subject: [Simnibs-discuss] headreco issue Hello , I?m trying to generate a head model in Windows 10. When using headreco I got the following error: OSError: Could not find tissue probability maps. Probably something went wrong with the Matlab call or SPM I saw that somebody else asked for this same error in the f?rum and he was suggested to install a newer versi?n. I just downloaded the last versi?n of SimNIBS (3.2) therefore this solution won?t work for me. Do you have any clue to avoid this problem? Many thanks in advance, Fabiola Alonso Provenance : Courrier pour Windows 10 ________________________________ Region Hovedstaden anvender de personoplysninger, du giver os i forbindelse med din henvendelse. Du kan l?se mere om form?let med anvendelsen samt dine rettigheder p? vores hjemmeside: www.regionh.dk/persondatapolitik -------------- next part -------------- An HTML attachment was scrubbed... URL: From fabiola.alonso-orozco at inserm.fr Wed Jun 30 09:05:48 2021 From: fabiola.alonso-orozco at inserm.fr (Fabiola ALONSO OROZCO) Date: Wed, 30 Jun 2021 09:05:48 +0200 Subject: [Simnibs-discuss] Install issue Message-ID: Hello, I'm trying to install SimNIBS 3.2.4 but I got this failure. Do you have any clue of what is happenning? Thank you in advance, Fabiola -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: InstallFailure.PNG Type: image/png Size: 69290 bytes Desc: not available URL: