From jerip101 at uni-duesseldorf.de Mon Jan 4 15:58:54 2021 From: jerip101 at uni-duesseldorf.de (Jennifer Rips) Date: Mon, 04 Jan 2021 15:58:54 +0100 Subject: [Simnibs-discuss] 4x1 montage Message-ID: <59754a14bb59c10570d8e03fef3deb84@uni-duesseldorf.de> Hi ! I use SimNibs for my bachelor thesis. The program is great, but I have a problem. I would like to use a 4x1 tDCS assembly with round electrodes. How can I set that the four outer electrodes have a certain distance to the center electrode? I would like to be able to enter coordinates for the center electrode and the four other round electrodes are located in a radius of 5cm. I would be very grateful for any help. Best regards, Jennifer Rips From 9300476 at ee.kntu.ac.ir Wed Jan 6 19:05:15 2021 From: 9300476 at ee.kntu.ac.ir (Nasireh Dayarian) Date: Wed, 6 Jan 2021 21:35:15 +0330 (IRST) Subject: [Simnibs-discuss] mesh resolution Message-ID: <207448833.4703158.1609956315904.JavaMail.zimbra@ee.kntu.ac.ir> Hi ! I use SimNibs for my PhD thesis. The mesh resolution is great but I need some various mesh resolution. I used [ https://simnibs.github.io/simnibs/build/html/documentation/command_line/headreco.html#headreco-docs | headreco ] to create mesh. I used headreco all ernie org/ernie_T1.nii.gz org/ernie_T2.nii.gz to create mesh. I know the mesh resolution can be changed with -v < density >, but I don't know where it must be added in above command. I would be very grateful for any help. Best regards, Nasireh -------------- next part -------------- An HTML attachment was scrubbed... URL: From dayarian.biom at gmail.com Wed Jan 6 22:12:48 2021 From: dayarian.biom at gmail.com (nasireh dayarian) Date: Thu, 7 Jan 2021 00:42:48 +0330 Subject: [Simnibs-discuss] mesh resolution Message-ID: Hi ! I use SimNibs for my PhD thesis. The mesh resolution is great but I need some various mesh resolution. I used headreco to create mesh. I used headreco all ernie org/ernie_T1.nii.gz org/ernie_T2.nii.gz to create mesh. I know the mesh resolution can be changed with -v < density >, but I don't know where it must be added in above command. I would be very grateful for any help. Best regards, Nasireh -------------- next part -------------- An HTML attachment was scrubbed... URL: From oupu at dtu.dk Fri Jan 8 08:41:05 2021 From: oupu at dtu.dk (Oula Puonti) Date: Fri, 8 Jan 2021 07:41:05 +0000 Subject: [Simnibs-discuss] mesh resolution In-Reply-To: References: Message-ID: Hi Nasireh, If you call: headreco all -h you can see all the options and how to call them. For increasing the mesh density you should call: headreco all -v 1.0 ernie org/ernie_T1.nii.gz org/ernie_T2.nii.gz where 1.0 is nodes/mm^2. Best, Oula ________________________________ From: Simnibs-discuss on behalf of nasireh dayarian Sent: Wednesday, January 6, 2021 10:12:48 PM To: discuss at simnibs.org Subject: [Simnibs-discuss] mesh resolution Hi ! I use SimNibs for my PhD thesis. The mesh resolution is great but I need some various mesh resolution. I used headreco to create mesh. I used headreco all ernie org/ernie_T1.nii.gz org/ernie_T2.nii.gz to create mesh. I know the mesh resolution can be changed with -v < density >, but I don't know where it must be added in above command. I would be very grateful for any help. Best regards, Nasireh -------------- next part -------------- An HTML attachment was scrubbed... URL: From jerip101 at uni-duesseldorf.de Fri Jan 8 11:35:55 2021 From: jerip101 at uni-duesseldorf.de (Jennifer Rips) Date: Fri, 08 Jan 2021 11:35:55 +0100 Subject: [Simnibs-discuss] 4x1 montage Message-ID: <3d36904dae35d8d0383c0e89510f5b4d@uni-duesseldorf.de> Hi ! I use SimNibs for my bachelor thesis. The program is great, but I have a problem. I would like to use a 4x1 tDCS assembly with round electrodes. How can I set that the four outer electrodes have a certain distance to the center electrode? I would like to be able to enter coordinates for the center electrode and the four other round electrodes are located in a radius of 5cm. I would be very grateful for any help. Best regards, Jennifer Rips From DXA869 at student.bham.ac.uk Tue Jan 12 12:38:26 2021 From: DXA869 at student.bham.ac.uk (DXA869 at student.bham.ac.uk) Date: Tue, 12 Jan 2021 11:38:26 +0000 Subject: [Simnibs-discuss] Moving n centimetres from electrode position Message-ID: <25d3b5c4eba54f0583b0afa798e339dc@student.bham.ac.uk> Dear users, I am trying to run a tDCS simulation on Simnibs, and I would like to place my active electrode exactly 3cm right to IZ. Is that possible? Best, Davide Aloi, Doctoral Researcher, Centre for Human Brain Health ? University of Birmingham -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Tue Jan 12 16:08:41 2021 From: axelt at drcmr.dk (Axel Thielscher) Date: Tue, 12 Jan 2021 16:08:41 +0100 Subject: [Simnibs-discuss] 4x1 montage In-Reply-To: <3d36904dae35d8d0383c0e89510f5b4d@uni-duesseldorf.de> References: <3d36904dae35d8d0383c0e89510f5b4d@uni-duesseldorf.de> Message-ID: <1124bf60-0fdc-8ec2-340e-908a755e00e9@drcmr.dk> Dear Jennifer, I have added the following python example: https://github.com/simnibs/simnibs/blob/master/simnibs/examples/simulations/tDCS_Nx1.py Best regards, Axel On 1/8/2021 11:35 AM, Jennifer Rips wrote: > Hi ! > I use SimNibs for my bachelor thesis. The program is great, but I have > a problem. I would like to use a 4x1 tDCS assembly with round > electrodes. How can I set that the four outer electrodes have a > certain distance to the center electrode? I would like to be able to > enter coordinates for the center electrode and the four other round > electrodes are located in a radius of 5cm. > > I would be very grateful for any help. > > Best regards, > > Jennifer Rips > _______________________________________________ > 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/ From axelt at drcmr.dk Tue Jan 12 16:20:55 2021 From: axelt at drcmr.dk (Axel Thielscher) Date: Tue, 12 Jan 2021 16:20:55 +0100 Subject: [Simnibs-discuss] Moving n centimetres from electrode position In-Reply-To: <25d3b5c4eba54f0583b0afa798e339dc@student.bham.ac.uk> References: <25d3b5c4eba54f0583b0afa798e339dc@student.bham.ac.uk> Message-ID: <2cb1cd8e-cb58-40eb-81bb-78d44bbdce56@drcmr.dk> Hi, I have just added the following python example: https://github.com/simnibs/simnibs/blob/master/simnibs/examples/simulations/tDCS_Nx1.py which you can adapt. Calling Ppos = get_surround_pos('Iz', 'ernie.msh', radius_surround = 30, N = 1, pos_dir_1stsurround = 'P10') will give you a position 30 mm right to Iz. Best regards, Axel On 1/12/2021 12:38 PM, DXA869 at student.bham.ac.uk wrote: > > Dear users, > > I am trying to run a tDCS simulation on Simnibs, and I would like to > place my active electrode exactly 3cm right to IZ. > > Is that possible? > > Best, > > Davide Aloi, > > Doctoral Researcher, > > Centre for Human Brain Health ? University of Birmingham > > > _______________________________________________ > 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: From yth888lynn at service.realfocusemail.com Tue Jan 12 05:15:07 2021 From: yth888lynn at service.realfocusemail.com (LiuYangLin) Date: Tue, 12 Jan 2021 12:15:07 +0800 (CST) Subject: [Simnibs-discuss] =?utf-8?q?shade_net_LiuYangLin?= Message-ID: <1610424907229_99612_82974_9143.sc-10_9_12_206-inbound0@service.realfocusemail.com> An HTML attachment was scrubbed... URL: From Kris.Baetens at vub.be Wed Jan 13 13:21:22 2021 From: Kris.Baetens at vub.be (Kris BAETENS) Date: Wed, 13 Jan 2021 12:21:22 +0000 Subject: [Simnibs-discuss] Working on a "generic" head model Message-ID: Dear SimNibs users, I want to compare several tDCS montages and assess field strength in particular ROI's, on a "generic" head model, prior to actually starting the study. I thought the MNI152 example mesh could serve perfectly for this purpose. However, I struggle with some very beginner technical issues. * Am I correct in assuming that this mesh is already in MNI space? * "Transform to MNI space" under simulation options fails, supposedly because the m2m folder doesn't contain the necessary information? * Similarly, the mni2subject_coords call in the example ROI script fails, again, I assume again because the m2m folder doesn't contain the necessary information? (I can get it to run without a problem on Ernie). * Is it possible to calculate mean field strength in an anatomical (e.g., atlas-based) ROI, rather than using the sphere-based approach? (I wanted to approach this from a "masking" angle, but am unsure how to proceed, as I cannot transform the standard head simulation to MNI space). Thank you very much for making this wonderful software and also making the tutorials publicly available on youtube! Kind regards, Kris Baetens -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Wed Jan 13 14:32:28 2021 From: axelt at drcmr.dk (Axel Thielscher) Date: Wed, 13 Jan 2021 14:32:28 +0100 Subject: [Simnibs-discuss] Working on a "generic" head model In-Reply-To: References: Message-ID: Dear Kris, please see my comments below. Best, Axel On 1/13/2021 1:21 PM, Kris BAETENS wrote: > > Dear SimNibs users, > > I want to compare several tDCS montages and assess field strength in > particular ROI?s, on a ?generic? head model, prior to actually > starting the study. I thought the MNI152 example mesh could serve > perfectly for this purpose. However, I struggle with some very > beginner technical issues. > > * Am I correct in assuming that this mesh is already in MNI space? > Yes. > > * ?Transform to MNI space? under simulation options fails, > supposedly because the m2m folder doesn?t contain the necessary > information? > As it is already in MNI space, there is no transformation required. Just use "Interpolate to a nifti volume" instead. > > * Similarly, the mni2subject_coords call in the example ROI script > fails, again, I assume again because the m2m folder doesn?t > contain the necessary information? (I can get it to run without a > problem on Ernie). > This call is not needed. Just use the coordinates without any transformation. > > * Is it possible to calculate mean field strength in an anatomical > (e.g., atlas-based) ROI, rather than using the sphere-based > approach? (I wanted to approach this from a ?masking? angle, but > am unsure how to proceed, as I cannot transform the standard head > simulation to MNI space). > Yes. The results which you get when using "Interpolate to a nifti volume" are already in MNI space, and you can apply any ROI that is in MNI space. Best regards, Axel > Thank you very much for making this wonderful software and also making > the tutorials publicly available on youtube! > > Kind regards, > > Kris Baetens > > > _______________________________________________ > 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: From heinesch at rhrk.uni-kl.de Tue Jan 19 10:30:59 2021 From: heinesch at rhrk.uni-kl.de (Christian Heinesch) Date: Tue, 19 Jan 2021 10:30:59 +0100 Subject: [Simnibs-discuss] Simulation of the magnetic field Message-ID: <202101190931.10J9V0xT168751@mailgw1.uni-kl.de> Hi, I want to use SimNibs for my bachelor thesis. The program is great, but I have a question. At TMS, the electric induced field can be simulated beautifully in Matlab. However, for my work the magnetic field is of relevance, for this I wanted to ask if there is any possibility to simulate the magnetic field of any coil. I would be very grateful for any help. Best regards, Christian Heinesch -------------- next part -------------- An HTML attachment was scrubbed... URL: From kristofferm at drcmr.dk Tue Jan 19 11:10:06 2021 From: kristofferm at drcmr.dk (Kristoffer Madsen) Date: Tue, 19 Jan 2021 11:10:06 +0100 Subject: [Simnibs-discuss] Simulation of the magnetic field In-Reply-To: <202101190931.10J9V0xT168751@mailgw1.uni-kl.de> References: <202101190931.10J9V0xT168751@mailgw1.uni-kl.de> Message-ID: The magnetic field (B-field) is largely uninfluenced by the volume conductor model. Therefore you should be able to visualize the magnetic field by exporting the dA/dt and then if you take the curl of this field you would have dB/dt for visualization. Note that you will have to calculate this curl manually in either Python or Matlab. Best, Kristoffer On Tue, 19 Jan 2021 at 10:53, Christian Heinesch wrote: > > Hi, > > I want to use SimNibs for my bachelor thesis. The program is great, but I have a > > question. > > At TMS, the electric induced field can be simulated beautifully in Matlab. However, for my work the magnetic field is of relevance, for this I wanted to ask if there is any possibility to simulate the magnetic field of any coil. > > > > I would be very grateful for any help. > > > > Best regards, > > Christian Heinesch > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss From inesviolante at gmail.com Wed Jan 20 11:59:01 2021 From: inesviolante at gmail.com (=?Windows-1252?Q?In=EAs_Violante?=) Date: Wed, 20 Jan 2021 10:59:01 +0000 Subject: [Simnibs-discuss] hippocampal segmentation to stl In-Reply-To: <43a5e105-ad9e-84cc-20bd-ab873047141e@drcmr.dk> References: <15b7a94e-0407-9f4f-a574-d2bb47b06e75@drcmr.dk> , <43a5e105-ad9e-84cc-20bd-ab873047141e@drcmr.dk> Message-ID: Dear Axel, Thanks for this. I ended up finding a work around using the c3d command from itk-SNAP. Leaving it here in case it is useful for someone else. All the best, Ines From: Axel Thielscher Date: Monday, 14 December 2020 at 18:17 To: In?s Violante , simnibs-discuss at drcmr.dk Subject: Re: [Simnibs-discuss] hippocampal segmentation to stl Dear Ines, the description in the simnibs documentation is not very clear, I am sorry for this. You can use nii2mesh -h to get a bit more information (not not much though). Please try calling it without the -ev. Best regards, Axel On 12/14/2020 12:51 PM, In?s Violante wrote: Hi Axel, Thanks for the quick reply. I tried that but with no luck. See command line output below. nii2msh -ev TIDES_P2T_S1_FreeSf/TIDES_P2T_S1/mri/lHippocampus.nii.gz TIDES_P2T_S1.msh lHipp.msh [ simnibs ]INFO: Creating tensor visualization Traceback (most recent call last): File "/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/nii2msh.py", line 92, in main() File "/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/nii2msh.py", line 71, in main aniso_tissues=[1, 2]) File "/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/simulation/cond.py", line 173, in cond2elmdata assert len(anisotropy_volume.shape) == 4 AssertionError Could this be because the volume is smaller than the expected from the T1 mesh? All the best, Ines -- Dr Ines Violante Lecturer in Psychological Neuroscience School of Psychology | Faculty of Health and Medical Sciences Room 32 AC 04 University of Surrey | Guildford GU2 7XH From: Axel Thielscher Date: Friday, 11 December 2020 at 20:39 To: simnibs-discuss at drcmr.dk , inesviolante at gmail.com Subject: Re: [Simnibs-discuss] hippocampal segmentation to stl Hi Ines, when you open the nifti-file in freeview, is it then coregistered with the _T1fs_conform.nii.gz which headreco creates? If not, you can first run freesurfer and use the T1 and T2 which freesurfer stores as input to headreco. You can then try the nii2msh tool, which puts the data from niftis into the mesh. Let us know in case you get stuck. Best regards, Axel On 12/9/2020 6:40 PM, In?s Violante wrote: Hello, I?ve just tried headreco and it is really cool. I would like to have a segmentation of the hippocampus in the same space as the meshes generated by headreco. I have the hippocampus segmentation from freesurfer aligned to the subject space. This is a .nii.gz file How can I now convert this to stl and have it in the same space as the other meshes generated by headreco? Thank you in advance! All the best, ines _______________________________________________ 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/ --> -- 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: From mana.biabanimoghadam at monash.edu Thu Jan 21 06:19:38 2021 From: mana.biabanimoghadam at monash.edu (Mana Biabani) Date: Thu, 21 Jan 2021 16:19:38 +1100 Subject: [Simnibs-discuss] Coil position Message-ID: Hi, I am using SimNIBS to simulate TMS-induced e-field and had two questions : 1- Is there any method to measure the exact distance between the coil and scalp surface? The 4mm default distance is not appropriate for my experiment; as the participants have EEG cap on and also there is a foam between the coil and the cap. Also, I?d like to account for the differences in the amount of hair, etc. I was thinking to measure the minimum euclidean distance between the coil centre and the scalp but as far as I understood the coil centre coordinates are actually scalp positions. So, it shouldn?t work. 2- My second question was about coil angle. I am using the angles that Brainsight provides to make the transformation matrix as below : [ m0n0 -m0n1 m0n2 coil.center(1) m1n0 -m1n1 m1n2 coil.center(2) m2n0 -m2n1 m2n2 coil.center(3)] . Could you please confirm if this matrix is correct. My understanding is that I need to inverse the y axis in Brainsight and it does not need any transformations (like MNI to subject space). Is that correct? Greatly appreciate your help in advance! Kind Regards, Mana --- MANA BIABANI Research Fellow Turner Institute for Brain and Mental Health Monash University 18 Innovation Walk Clayton VIC 3800 Australia E: mana.biabanimoghadam at monash.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From mana.biabanimoghadam at monash.edu Fri Jan 22 00:03:43 2021 From: mana.biabanimoghadam at monash.edu (Mana Biabani) Date: Fri, 22 Jan 2021 10:03:43 +1100 Subject: [Simnibs-discuss] Coil position _question modified In-Reply-To: References: Message-ID: <5825440A-AFB6-47AB-819D-096494B68FF1@monash.edu> Hi again! I apologise for the additional email. I would like to modify my question below regarding the coil position. Would appreciate if you could ignore my previous email and help me with the points below: > I am using SimNIBS to simulate TMS-induced e-field and had two questions : > > 1- Is there any method to measure the exact distance between the coil and scalp surface? The 4mm default distance is not appropriate for my experiment; as the participants have EEG cap on and also there is a foam between the coil and the cap. Also, I?d like to account for the differences in the hair volume, etc. I was thinking to measure the minimum euclidean distance between the coil centre and the scalp coordinates but as far as I understood the coil centre is actually a scalp position. So, it shouldn?t work. > > 2- My second question was about the coil orientation (in a more accurate way than choosing a reference electrode ?). I am using Brainsight to get the information about the coil position, but not sure which outputs represent coil angels around different axes. I guess I can use [m0n0 m0n1 m0n2; m1n0 m1n1 m1n2; m2n0 m2n1 m2n2 ] from Brainsight to make the transformation matrix, is that correct? If so, could you please let me know how I should modify them to be compatible with the coil axes in SimNIBS. > Kind regards, Mana --- MANA BIABANI Research Fellow Turner Institute for Brain and Mental Health Monash University 18 Innovation Walk Clayton VIC 3800 Australia E: mana.biabanimoghadam at monash.edu > On 21 Jan 2021, at 4:19 pm, Mana Biabani wrote: > > Hi, > > I am using SimNIBS to simulate TMS-induced e-field and had two questions : > > 1- Is there any method to measure the exact distance between the coil and scalp surface? The 4mm default distance is not appropriate for my experiment; as the participants have EEG cap on and also there is a foam between the coil and the cap. Also, I?d like to account for the differences in the amount of hair, etc. I was thinking to measure the minimum euclidean distance between the coil centre and the scalp but as far as I understood the coil centre coordinates are actually scalp positions. So, it shouldn?t work. > > 2- My second question was about coil angle. I am using the angles that Brainsight provides to make the transformation matrix as below : > > [ m0n0 -m0n1 m0n2 coil.center(1) > m1n0 -m1n1 m1n2 coil.center(2) > m2n0 -m2n1 m2n2 coil.center(3)] . > > Could you please confirm if this matrix is correct. My understanding is that I need to inverse the y axis in Brainsight and it does not need any transformations (like MNI to subject space). Is that correct? > > Greatly appreciate your help in advance! > > Kind Regards, > Mana > > > --- > MANA BIABANI > Research Fellow > > Turner Institute for Brain and Mental Health > Monash University > 18 Innovation Walk > Clayton VIC 3800 > Australia > > E: mana.biabanimoghadam at monash.edu > > > > > > > > > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From 1155138422 at link.cuhk.edu.hk Mon Jan 25 04:42:14 2021 From: 1155138422 at link.cuhk.edu.hk (TI, Chun Hang Eden) Date: Mon, 25 Jan 2021 03:42:14 +0000 Subject: [Simnibs-discuss] Questions regarding the Fsaverage space transformation , and electrode coordinates Message-ID: Dear Sir/Madam, I am currently running simulation analysis using the Fsaverage space provided by SIMNIBS. I want to study the relationship between the distance of electrodes and the electric field on that space. Is there a way to transform the MNI/native coordinates to the Fsaverage coordinates through matlab script? In addition, I am also interested in how electrode geometry and their effect of stimulation. Currently the coordinates of electrodes are stored in .geo file. Is there a way to read these coordinates using MATLAB? Look forward to your reply, and thank you very much. Best regards, Eden -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Tue Jan 26 20:19:51 2021 From: axelt at drcmr.dk (Axel Thielscher) Date: Tue, 26 Jan 2021 20:19:51 +0100 Subject: [Simnibs-discuss] Coil position _question modified In-Reply-To: <5825440A-AFB6-47AB-819D-096494B68FF1@monash.edu> References: <5825440A-AFB6-47AB-819D-096494B68FF1@monash.edu> Message-ID: Dear Mana: On 1/22/2021 12:03 AM, Mana Biabani wrote: > Hi again! > > I apologise for the additional email. I would like to modify my > question below regarding the coil position. > > Would appreciate if you could ignore my previous email and help me > with the points below: > >> I am using SimNIBS to simulate TMS-induced e-field and had two >> questions : >> >> 1-?Is there any method to measure the exact distance between the coil >> and scalp surface? The 4mm default distance is not appropriate for my >> experiment; as the participants have EEG cap on and also there is a >> foam between the coil and the cap. Also, I?d like to account for the >> differences in the hair volume, etc. ?I was thinking to measure the >> minimum euclidean distance between the coil centre and the scalp >> coordinates but as far as I understood the coil centre is actually a >> scalp position. So, it shouldn?t work. When you have measured the distance physically during your experiment or can estimate it otherwise, you can update the distance used by SimNIBS by the proper value. See "distance" on https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/position.html Example : pos.distance = 10 --> 10 mm distance to skin Note that you can also enter coordinates instead of electrode positions for the centre and pos_ydir. >> >> 2- My second question was about the coil orientation (in a more >> accurate way than choosing a reference electrode ?). I am using >> Brainsight to get the information about the coil position, but not >> sure which outputs represent coil angels around different axes. I >> guess I can use [m0n0 m0n1 m0n2; ?m1n0 m1n1 m1n2; m2n0 m2n1 m2n2 ] >> from Brainsight to make the transformation matrix, is that correct? >> If so, could you please let me know how I should modify them to be >> compatible with the coil axes in SimNIBS. When you have neuronavigation positions, you can directly set the *matsimnibs *(also see https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/position.html.) Please also see https://simnibs.github.io/simnibs/build/html/_downloads/f0b89a9aa2f494cfe8e4dfd5d455e80e/coil_axesorientation.pdf for a visualizatoin of the coil coordinate system used by SimNIBS. I think that you can use Lox X, Loc Y & Loc Z and the m0n0 m0n1 m0n2, m1n0 ...... to directly set up the matsimnibs, but you will likely have to exchange some of axes (i.e. m0 might not correspond to px, but maybe -pz or so, depending on how the convention in Brainsight is). Hope this helps. Best regards, Axel >> > > Kind regards, > Mana > > > > --- > *MANA BIABANI* > Research Fellow > > *Turner Institute for Brain and Mental Health* > Monash University > 18 Innovation Walk > Clayton VIC 3800 > Australia > > E: mana.biabanimoghadam at monash.edu > > > > > >> On 21 Jan 2021, at 4:19 pm, Mana Biabani >> > > wrote: >> >> Hi, >> >> I am using SimNIBS to simulate TMS-induced e-field and had two >> questions : >> >> 1-?Is there any method to measure the exact distance between the coil >> and scalp surface? The 4mm default distance is not appropriate for my >> experiment; as the participants have EEG cap on and also there is a >> foam between the coil and the cap. Also, I?d like to account for the >> differences in the amount of hair, etc. ?I was thinking to measure >> the minimum euclidean distance between the coil centre and the scalp >> but as far as I understood the coil centre coordinates are actually >> scalp positions. So, it shouldn?t work. >> >> 2- My second question was about coil angle. I am using the angles >> that Brainsight provides to make the transformation matrix as below : >> >> [ m0n0-m0n1m0n2 coil.center(1) >> ?m1n0-m1n1m1n2coil.center(2) >> ?m2n0-m2n1m2n2coil.center(3)] . >> >> Could you please confirm if this matrix is correct. ?My understanding >> is that I need to inverse the y axis in Brainsight and it does not >> need any transformations (like MNI to subject space). Is that correct? >> >> Greatly appreciate your help in advance! >> >> Kind Regards, >> Mana >> >> >> --- >> *MANA BIABANI* >> Research Fellow >> >> *Turner Institute for Brain and Mental Health* >> Monash University >> 18 Innovation Walk >> Clayton VIC 3800 >> Australia >> >> E: mana.biabanimoghadam at monash.edu >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > > _______________________________________________ > 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: From phcunha at yahoo.com Sat Jan 30 18:46:29 2021 From: phcunha at yahoo.com (Pedro Cunha) Date: Sat, 30 Jan 2021 14:46:29 -0300 Subject: [Simnibs-discuss] Problems with Mac Catalina References: <73C31DEA-B724-4F59-AD43-4B12A0CF1CF3.ref@yahoo.com> Message-ID: <73C31DEA-B724-4F59-AD43-4B12A0CF1CF3@yahoo.com> Hi, I?m a new Simnibs user on a Mac Catalina 10.15.4. After follow the tutorial, the GMesh window doesn?t have the options. And the simulations appear all with a blank screen. Is there an update or something like that? Thanks Pedro Cunha -------------- next part -------------- An HTML attachment was scrubbed... URL: