From martin.bardhi at ucalgary.ca Wed Jun 1 23:32:26 2022 From: martin.bardhi at ucalgary.ca (Martin Bardhi) Date: Wed, 1 Jun 2022 21:32:26 +0000 Subject: [Simnibs-discuss] 4x1 Optamization Message-ID: Hello, This is Martin B, a University of Calgary researcher using simnibs tdcs optamization modeling for my project. Thank you for the fast response on my last question. I was now wondering if there was any way to optimize the electrode placement for a 4x1 montage, where you could set one anode or cathode to be at +/- 1 mA, and 4 adjacent ones at -/+ 0.25mA, but with an optimized position. Thank you, Martin -------------- next part -------------- An HTML attachment was scrubbed... URL: From lena.marie.kuczka at uni-oldenburg.de Sun Jun 5 22:30:42 2022 From: lena.marie.kuczka at uni-oldenburg.de (Lena Kuczka) Date: Sun, 5 Jun 2022 22:30:42 +0200 Subject: [Simnibs-discuss] tDCS optimization with --no-cat headmesh Message-ID: Hello, I am trying to simulate an optimized tDCS montage for a distributed target, but have encountered a problem in the last step of the process. I've manually edited the segmentation masks to include a lesion I segmented separately, so I don't use CAT12 for meshing. Unfortunately when I know run the simulation with that head mesh, I get this error: ??? numpy.linalg.LinAlgError: Singular matrix This only happens for meshes created with headreco all --no-cat, as far as I'm aware. Could that be a problem with the leadfield or am I missing something? Thank you in advance, Lena From adallave at g.ucla.edu Wed Jun 8 01:52:57 2022 From: adallave at g.ucla.edu (Alessandra Dallavecchia) Date: Tue, 7 Jun 2022 16:52:57 -0700 Subject: [Simnibs-discuss] Nexstim TMS simulation Message-ID: Dear all, I have been working on trying to do some e-field simulations for our TMS-EEG data, but have been running into a couple of issues. We use a Nexstim system (NBT 2.2), so my first question would be if there was a reasonable approximation for a coil configuration file that I could use, or how I might be able to create one specific to the Nexstim figure-8 coil. My second question is in regards to the coil position coordinates. Nexstim outputs three coordinates for coil location, direction, and normal in mm. However, I've noticed that these coordinates are wildly different from those that SimNIBS gives me when I manually place a point on the GUI as close to the center of the coil. Both are in mm and are in subject space. I know that their coordinates line up with FreeSurfer as I do source modeling for my EEG data, and I've tried a number of permutations (e.g., switching x/y/z axes), but nothing seems to get me close in SimNIBS to this actual coil position when I use the Nexstim output coords. *Left Parietal Stimulation Site from the Nexstim Neuronavigation* [image: Coil direction.png] *Similar Coil Position in the SimNIBS GUI:* [image: Coil Pos SimNIBS.png] Thank you, *--* *Alessandra DallaVecchia, M.A.* PhD candidate, Cognitive Neuroscience UCLA Department of Psychology She/her *If this email finds you outside of your normal business hours, please do not feel obligated to reply and feel free to respond when you're next working or in front of a computer.* -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Coil direction.png Type: image/png Size: 292402 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Coil Pos SimNIBS.png Type: image/png Size: 239091 bytes Desc: not available URL: From benjamin.tessler at downstate.edu Wed Jun 8 20:16:59 2022 From: benjamin.tessler at downstate.edu (Benjamin Tessler) Date: Wed, 8 Jun 2022 18:16:59 +0000 Subject: [Simnibs-discuss] SimNibs simple volumes Message-ID: Hi, I?m trying to just stimulate a block. What CAD do you recommend to use? I?m using Autodesk fusion 360 to make STL files. Then I use gmesh to make a msh file, but it won?t import into simnibs. Is there a simple way to make simple volumes? Best, Ben Sent from Mail for Windows ________________________________ The contents of this email message and any attachments are confidential and are intended solely for the addressee. The information may also be legally privileged. This transmission is sent in trust, for the sole purpose of delivery to the intended recipient. If you have received this transmission in error, any use, reproduction or dissemination of this transmission is strictly prohibited. If you are not the intended recipient, please immediately notify sender by reply email or by (718) 270-HELP. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bellabingbing.zhang at connect.polyu.hk Thu Jun 9 16:31:11 2022 From: bellabingbing.zhang at connect.polyu.hk (ZHANG, bellabingbing [Student]) Date: Thu, 9 Jun 2022 14:31:11 +0000 Subject: [Simnibs-discuss] ROI analysis using MNI coordinates using the middle cortical surfaces Message-ID: Dear Madam or Sir, Hope this email finds you well. I am doing the TMS E-fields simulation. When I analysed the simulation results, I noticed we can use the default mesh file for ROI analysis using MNI coordinate or use middle cortical surfaces for ROI analysis based on atlas. However, I want to analyse the normal and tangent comments which are only stored in the middle cortical surfaces file. Can I use MNI coordinate for ROI analysis in this file? Looking forward to your reply! Best Regards, Bella [https://www.polyu.edu.hk/emaildisclaimer/85A-PolyU_Email_Signature.jpg] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information. -------------- next part -------------- An HTML attachment was scrubbed... URL: From simayuner.nsc at gmail.com Fri Jun 10 12:54:14 2022 From: simayuner.nsc at gmail.com (=?UTF-8?Q?Simay_=C3=9Cner?=) Date: Fri, 10 Jun 2022 13:54:14 +0300 Subject: [Simnibs-discuss] tRNS & bilateral hMT+ stimulation Message-ID: Hello, First of all, thank you for developing this simulation software as it is really useful for us researchers! I am a PhD student who will use tES soon, but both the project and this stimulation/simulation literature is very new to me, so I need some clarifications if you don't mind helping. We have NeuroConn DC-Stimulator-Plus here in the lab, and I want to stimulate hMT+ (V5) *bilaterally *with tRNS. The problem is that only* one-channel stimulation* is possible with this device. First, - Because I am going to use tRNS mode instead of giving a direct current stimulation, I couldn't be sure that the simulation I run on this software is applicable for tACS experiments, especially for tRNS. If it is not applicable, is there anything you can recommend to me to visualize tRNS effect with one channel stimulation? I want to be sure about the regions that will be affected by my stimulation, and if tDCS simulations are not applicable for this, I need to find another way. Second, - If applicable for tRNS, when I run simulations for tDCS -because of one channel stimulation- I saw that a huge area between my two stimulation sites (probably around PO7-PO8 electrode regions) are substantially affected by stimulation, regardless of the current applied. I am sure that you are much more familiar with the procedure, so I wanted to ask if there is anything you can recommend to do to stimulate *only electrode positions *(and near areas of course) but not the regions in between with tRNS, considering that I don't have any chance to use multichannel systems. I have to note that the smallest electrodes I have are rectangular 3cm x 3cm (and sponges), and new orders are delivered to Turkey in several months which will, unfortunately, affect my schedule. Any response and recommendation will be very helpful. Thank you for your time, Kind regards, -- *Simay ?ner* PhD Student in Neuroscience Bilkent University, Ankara, Turkey -------------- next part -------------- An HTML attachment was scrubbed... URL: From simayuner.nsc at gmail.com Fri Jun 10 13:04:54 2022 From: simayuner.nsc at gmail.com (=?UTF-8?Q?Simay_=C3=9Cner?=) Date: Fri, 10 Jun 2022 14:04:54 +0300 Subject: [Simnibs-discuss] tRNS & bilateral hMT+ stimulation Message-ID: Hello, First of all, thank you for developing this simulation software as it is really useful for us researchers! I am a PhD student who will use tES soon, but both the project and this stimulation/simulation literature is very new to me, so I need some clarifications if you don't mind helping. We have NeuroConn DC-Stimulator-Plus here in the lab, and I want to stimulate hMT+ (V5) *bilaterally *with tRNS. The problem is that only* one-channel stimulation* is possible with this device. First, - Because I am going to use tRNS mode instead of giving a direct current stimulation, I couldn't be sure that the simulation I run on this software is applicable for tACS experiments, especially for tRNS. If it is not applicable, is there anything you can recommend to me to visualize tRNS effect with one channel stimulation? I want to be sure about the regions that will be affected by my stimulation, and if tDCS simulations are not applicable for this, I need to find another way. Second, - If applicable for tRNS, when I run simulations for tDCS -because of one channel stimulation- I saw that a huge area between my two stimulation sites (probably around PO7-PO8 electrode regions) are substantially affected by stimulation, regardless of the current applied. I am sure that you are much more familiar with the procedure, so I wanted to ask if there is anything you can recommend to do to stimulate *only electrode positions *(and near areas of course) but not the regions in between with tRNS, considering that I don't have any chance to use multichannel systems. I have to note that the smallest electrodes I have are rectangular 3cm x 3cm (and sponges), and new orders are delivered to Turkey in several months which will, unfortunately, affect my schedule. Any response and recommendation will be very helpful. Thank you for your time, Kind regards, -- *Simay ?ner* PhD Student in Neuroscience Bilkent University, Ankara, Turkey -------------- next part -------------- An HTML attachment was scrubbed... URL: From utkarshpancholi6387 at gmail.com Mon Jun 13 10:10:31 2022 From: utkarshpancholi6387 at gmail.com (Utkarsh Pancholi) Date: Mon, 13 Jun 2022 13:40:31 +0530 Subject: [Simnibs-discuss] Head mesh not generated ( Error msg attached ) Message-ID: Hi, I tried to make mesh generation using headreco all command in command line. Here is the error. *Traceback (most recent call last): File "C:\Users\Administrator\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\cli\headreco.py", line 13, in main() File "C:\Users\Administrator\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\cli\headreco.py", line 10, in main headmodel(sys.argv) File "C:\Users\Administrator\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\msh\headreco.py", line 730, in headmodel "Gmsh failed meshing one or more volumes. "RuntimeError: Gmsh failed meshing one or more volumes. Please try running headreco again increasing the '-v' option (eg. -v 1.0). Type 'headreco all -h' for more information* What can be done for this? Also, I wanted to know if structural MRI images above 45 MB can be processed without any errors as i mentioned above. But I have processed T1 weighted structural MRI image having a size of 38MB. is having the above error. I want to know what is the minimum criteria for the T1 weighted MRI image's size. Runtime error suggested increasing vertex density to 1.0. (-V).. What is the consequence of increasing vertex density on electric field strength distribution? Waiting for the help. ----------------------------------------------------------------------------------------------------- UTKARSH V. PANCHOLI L.D COLLEGE OF ENGINEERING AHMEDABAD-380015 -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Mon Jun 13 10:30:46 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Mon, 13 Jun 2022 10:30:46 +0200 Subject: [Simnibs-discuss] Head mesh not generated ( Error msg attached ) In-Reply-To: References: Message-ID: Hi, the image size in MB does not really matter. It's more about the resolution, where too small voxel sizes might be a challenge. Usual resolutions range between 0.75 to 1.0 mm. Increasing the vertex density makes the mesh larger, thus the simulations slower but more accurate. Just try out the suggested increase to see whether your problem is resolved. Best regards, Axel On 13-06-2022 10:10, Utkarsh Pancholi wrote: > Hi, > > I tried to make mesh generation using headreco all command in command > line. Here is the error. > > *Traceback (most recent call last): > ? File > "C:\Users\Administrator\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\cli\headreco.py", > line 13, in > ? ? main() > ? File > "C:\Users\Administrator\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\cli\headreco.py", > line 10, in main > ? ? headmodel(sys.argv) > ? File > "C:\Users\Administrator\SimNIBS-3.2\simnibs_env\lib\site-packages\simnibs\msh\headreco.py", > line 730, in headmodel > ? ? "Gmsh failed meshing one or more volumes. " > RuntimeError: Gmsh failed meshing one or more volumes. Please try > running headreco again increasing the '-v' option (eg. -v 1.0). Type > 'headreco all -h' for more information* > * > * > What can be done for?this? > > Also,?I wanted to know if structural MRI images above 45 MB can be > processed without any errors as i mentioned above. But I have > processed T1 weighted structural?MRI image having a size of 38MB. is > having the above error. > > I want to know what is the minimum criteria for the T1 weighted MRI > image's size. > > > Runtime error suggested increasing vertex density to 1.0. (-V).. What > is the consequence?of increasing vertex density on electric field > strength distribution? > > Waiting for the help. > ----------------------------------------------------------------------------------------------------- > UTKARSH V. PANCHOLI > L.D COLLEGE OF ENGINEERING > AHMEDABAD-380015 > > _______________________________________________ > 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 Mon Jun 13 10:42:33 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Mon, 13 Jun 2022 10:42:33 +0200 Subject: [Simnibs-discuss] tRNS & bilateral hMT+ stimulation In-Reply-To: References: Message-ID: <3d80a27d-2802-051e-4ea5-ce3418f70cf0@drcmr.dk> Hi, attached are a few slides on how tDCS simulations relate to tACS and tRNS. As long as you have only one one-channel stimulator, bilateral stimulation will be unfocal. You can consider combining two one-channel stimulators to have to center-surround montages above the two V5. Best, Axel On 10-06-2022 13:04, Simay ?ner wrote: > Hello, > > First of all, thank you for developing this simulation software as it > is really useful for us researchers! > > I am a PhD student who will use tES soon, but both the project and > this stimulation/simulation literature is very new to me, so I need > some clarifications if you don't mind helping. > > We have?NeuroConn DC-Stimulator-Plus > ?here in the lab, > and I want to stimulate hMT+ (V5) *bilaterally *with tRNS. The problem > is that only_?one-channel stimulation_?is possible with this device. > > First, > - Because I am going to use tRNS mode instead of giving a direct > current stimulation, I couldn't be sure that the simulation I run on > this software is applicable for tACS experiments, especially for tRNS. > If it is not applicable, is there anything you can recommend to me to > visualize tRNS effect with one channel stimulation? I want to be sure > about the regions that will be affected by my stimulation, and if tDCS > simulations are not applicable for this, I need to find another way. > > Second, > - If applicable for tRNS, when I run simulations for tDCS -because of > one channel stimulation- I saw that a huge area between my two > stimulation sites (probably around PO7-PO8 electrode regions) are > substantially affected by stimulation, regardless of the current > applied. I am sure that you are much more familiar with the procedure, > so I wanted to ask if there is anything you can recommend to do to > stimulate *only electrode positions *(and near areas of course)?but > not the regions in between with tRNS, considering that I don't have > any chance to use multichannel systems. > > I have to note that the smallest electrodes I have are rectangular 3cm > x 3cm (and sponges), and new orders are delivered to Turkey in several > months which will, unfortunately, affect my schedule. > > Any response and recommendation will be very helpful. > Thank you for your time, > > Kind regards, > -- > *Simay ?ner* > PhD Student in Neuroscience > Bilkent University, Ankara, Turkey > > > _______________________________________________ > 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: Thielscher_BrainBox_Saturday_2019_trns.pdf Type: application/pdf Size: 1156756 bytes Desc: not available URL: From simayuner.nsc at gmail.com Mon Jun 13 10:48:00 2022 From: simayuner.nsc at gmail.com (=?utf-8?Q?Simay_=C3=9Cner?=) Date: Mon, 13 Jun 2022 11:48:00 +0300 Subject: [Simnibs-discuss] tRNS & bilateral hMT+ stimulation In-Reply-To: <3d80a27d-2802-051e-4ea5-ce3418f70cf0@drcmr.dk> References: <3d80a27d-2802-051e-4ea5-ce3418f70cf0@drcmr.dk> Message-ID: <786FB0D8-A5F7-49DC-AEF2-03870B5CC73C@gmail.com> Hello Dr. Thielscher, Thanks for response. I will see if I order new electrodes for better focality. Kind regards, B. Simay ?ner PhD Student Interdisciplinary Neuroscience Program - Bilkent University simay.uner at bilkent.edu.tr simay.uner at umram.bilkent.edu.tr > On 13 Jun 2022, at 11:42, Axel Thielscher wrote: > > Hi, > > attached are a few slides on how tDCS simulations relate to tACS and tRNS. > > As long as you have only one one-channel stimulator, bilateral stimulation will be unfocal. You can consider combining two one-channel stimulators to have to center-surround montages above the two V5. > > Best, > > Axel > > > > On 10-06-2022 13:04, Simay ?ner wrote: >> Hello, >> >> First of all, thank you for developing this simulation software as it is really useful for us researchers! >> >> I am a PhD student who will use tES soon, but both the project and this stimulation/simulation literature is very new to me, so I need some clarifications if you don't mind helping. >> >> We have?NeuroConn DC-Stimulator-Plus here in the lab, and I want to stimulate hMT+ (V5) bilaterally with tRNS. The problem is that only one-channel stimulation is possible with this device. >> >> First, >> - Because I am going to use tRNS mode instead of giving a direct current stimulation, I couldn't be sure that the simulation I run on this software is applicable for tACS experiments, especially for tRNS. If it is not applicable, is there anything you can recommend to me to visualize tRNS effect with one channel stimulation? I want to be sure about the regions that will be affected by my stimulation, and if tDCS simulations are not applicable for this, I need to find another way. >> >> Second, >> - If applicable for tRNS, when I run simulations for tDCS -because of one channel stimulation- I saw that a huge area between my two stimulation sites (probably around PO7-PO8 electrode regions) are substantially affected by stimulation, regardless of the current applied. I am sure that you are much more familiar with the procedure, so I wanted to ask if there is anything you can recommend to do to stimulate only electrode positions (and near areas of course) but not the regions in between with tRNS, considering that I don't have any chance to use multichannel systems. >> >> I have to note that the smallest electrodes I have are rectangular 3cm x 3cm (and sponges), and new orders are delivered to Turkey in several months which will, unfortunately, affect my schedule. >> >> Any response and recommendation will be very helpful. >> Thank you for your time, >> >> Kind regards, >> -- >> Simay ?ner >> PhD Student in Neuroscience >> Bilkent University, Ankara, Turkey >> >> >> >> _______________________________________________ >> 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 Mon Jun 13 11:53:15 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Mon, 13 Jun 2022 11:53:15 +0200 Subject: [Simnibs-discuss] ROI analysis using MNI coordinates using the middle cortical surfaces In-Reply-To: References: Message-ID: Hi, the fsaverage template is quite well aligned with MNI space. You can thus tryo to apply MNI coordinates and do the ROI analyses on the results mapped to fsaverage space. Best regards, Axel On 09-06-2022 16:31, ZHANG, bellabingbing [Student] wrote: > > Dear Madam or Sir, > > Hope this email finds you well. > > I am doing the TMS E-fields simulation. When I ?analysed the > simulation results, I noticed we can use the default mesh file for ROI > analysis using MNI coordinate or use middle cortical surfaces for ROI > analysis based on atlas. > > However, I want to analyse the normal and tangent comments which are > only stored in the middle cortical surfaces file. Can I use MNI > coordinate for ROI analysis in this file? > > Looking forward to your reply! > > Best Regards, > > Bella > > > /Disclaimer:/ > > /This message (including any attachments) contains confidential > information intended for a specific individual and purpose. If you are > not the intended recipient, you should delete this message and notify > the sender and The Hong Kong Polytechnic University (the University) > immediately. Any disclosure, copying, or distribution of this message, > or the taking of any action based on it, is strictly prohibited and > may be unlawful./ > > /The University specifically denies any responsibility for the > accuracy or quality of information obtained through University E-mail > Facilities. Any views and opinions expressed are only those of the > author(s) and do not necessarily represent those of the University and > the University accepts no liability whatsoever for any losses or > damages incurred or caused to any party as a result of the use of such > information./ > > > _______________________________________________ > 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 Mon Jun 13 11:57:16 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Mon, 13 Jun 2022 11:57:16 +0200 Subject: [Simnibs-discuss] SimNibs simple volumes In-Reply-To: References: Message-ID: <32efe2dc-a83d-298f-541a-cc05a6f5319b@drcmr.dk> Hi Benjamin, please try out simnibs 4 which is available as beta release. https://github.com/simnibs/simnibs/releases/tag/v4.0-beta1 It has new options to use custom-made meshes. After installation, click on index.html in the docs-folder to see the documentation for simnibs 4. Then follow the tutorial "How to create and use a custom mesh". Best, Axel On 08-06-2022 20:16, Benjamin Tessler wrote: > > Hi, > > I?m trying to just stimulate a block. What CAD do you recommend to > use? I?m using Autodesk fusion 360 to make STL files. Then I use gmesh > to make a msh file, but it won?t import into simnibs. Is there a > simple way to make simple volumes? > > Best, > > Ben > > Sent from Mail for > Windows > > > ------------------------------------------------------------------------ > > The contents of this email message and any attachments are > confidential and are intended solely for the addressee. The > information may also be legally privileged. This transmission is sent > in trust, for the sole purpose of delivery to the intended recipient. > If you have received this transmission in error, any use, reproduction > or dissemination of this transmission is strictly prohibited. If you > are not the intended recipient, please immediately notify sender by > reply email or by (718) 270-HELP. > > _______________________________________________ > 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 Mon Jun 13 12:08:46 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Mon, 13 Jun 2022 12:08:46 +0200 Subject: [Simnibs-discuss] Nexstim TMS simulation In-Reply-To: References: Message-ID: <467c0706-7a20-586a-2dc0-19273c1a6523@drcmr.dk> Hi Alessandra, we don't have coil models for Nextim coils. If the company is willing to share detailed information about the coil geometry, we can likely help you to get a reasonable model, though. Regarding the coil position coordinates: Please use headreco, not mri2mesh to create the head model, because headreco doesn't change the header information of the T1 image. In addition, read the same T1 image into the neuronavigation system. If this still results in different positions for the coil center, then the Nexstim system interally changes the coordinate system of the image. In that case, we would need information from Nexstim on their internal coordinate system to be able to resolve that issue. Best regards, Axel On 08-06-2022 01:52, Alessandra Dallavecchia wrote: > Dear all, > > I have been working on trying to do some e-field simulations for our > TMS-EEG data, but have been running into a couple of issues. > > We use a Nexstim system (NBT 2.2), so my first question would be if > there was a reasonable approximation for a coil configuration file > that I could use, or how I might be able to create one specific to the > Nexstim figure-8 coil. > > My second question is in regards to the coil position coordinates. > Nexstim outputs three coordinates for coil location, direction, and > normal in mm. However, I've noticed that these coordinates are wildly > different from those that SimNIBS gives me when I manually place a > point on the GUI as close to the center of the coil. Both are in mm > and are in subject space. I know that their coordinates line up with > FreeSurfer as I do source modeling for my EEG data, and I've tried a > number of permutations (e.g., switching x/y/z axes), but nothing seems > to get me close in SimNIBS to this actual coil position when I use the > Nexstim output coords. > > *Left Parietal Stimulation Site from the Nexstim Neuronavigation* > Coil direction.png > > *Similar Coil Position in the SimNIBS GUI:* > > Coil Pos SimNIBS.png > > Thank you, > > /--/ > *Alessandra DallaVecchia, M.A.* > PhD candidate, Cognitive Neuroscience > UCLA Department of Psychology > She/her > > /If this email finds you outside of your normal business hours, please > do not feel obligated to reply and feel free to respond when you're > next working or in front of a computer./ > > _______________________________________________ > 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: Coil%20direction.png Type: image/png Size: 292402 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Coil%20Pos%20SimNIBS.png Type: image/png Size: 239091 bytes Desc: not available URL: From axelt at drcmr.dk Mon Jun 13 12:45:03 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Mon, 13 Jun 2022 12:45:03 +0200 Subject: [Simnibs-discuss] tDCS optimization with --no-cat headmesh In-Reply-To: References: Message-ID: <0b70219b-ef0c-75f0-70b4-02eb61da42bd@drcmr.dk> Hi Lena, the distributed optimization requires that you have a cortical surface reconstruction. The other optimization methods will still work without surfaces, even though you will have to update the scripts for leadfield creation and optimization to specify that you want to use volume information instead surfaces. Best regards, Axel On 05-06-2022 22:30, Lena Kuczka wrote: > Hello, > > I am trying to simulate an optimized tDCS montage for a distributed > target, but have encountered a problem in the last step of the process. > > I've manually edited the segmentation masks to include a lesion I > segmented separately, so I don't use CAT12 for meshing. Unfortunately > when I know run the simulation with that head mesh, I get this error: > > ??? numpy.linalg.LinAlgError: Singular matrix > > This only happens for meshes created with headreco all --no-cat, as > far as I'm aware. Could that be a problem with the leadfield or am I > missing something? > > Thank you in advance, > Lena > > > _______________________________________________ > 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/ From axelt at drcmr.dk Mon Jun 13 15:08:17 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Mon, 13 Jun 2022 15:08:17 +0200 Subject: [Simnibs-discuss] 4x1 Optamization In-Reply-To: References: Message-ID: Hi Martin, there is currently no optimization specific for 4x1 electrode positions. The closest you can get is to optimize with: max_total_current: 2 mA max_individual_current: 1 mA max_active_electrodes: 4 and for the target: directions = None and then try several values for the intensity of the target. Best regards, Axel On 01-06-2022 23:32, Martin Bardhi wrote: > > Hello, > > This is Martin B, a University of Calgary researcher using simnibs > tdcs optamization modeling for my project. Thank you for the fast > response on my last question. I was now wondering if there was any way > to optimize the electrode placement for a 4x1 montage, where you could > set one anode or cathode to be at +/- 1 mA, and 4 adjacent ones at -/+ > 0.25mA, but with an optimized position. > > Thank you, > > Martin > > > _______________________________________________ > 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 bellabingbing.zhang at connect.polyu.hk Tue Jun 14 16:40:42 2022 From: bellabingbing.zhang at connect.polyu.hk (ZHANG, bellabingbing [Student]) Date: Tue, 14 Jun 2022 14:40:42 +0000 Subject: [Simnibs-discuss] =?gb2312?b?u9i4tDogIFJPSSBhbmFseXNpcyB1c2luZyBN?= =?gb2312?b?TkkgY29vcmRpbmF0ZXMgdXNpbmcgdGhlIG1pZGRsZSBjb3J0aWNhbCBzdXJm?= =?gb2312?b?YWNlcw==?= In-Reply-To: References: Message-ID: Dear Dr. Thielscher, Thanks for your reply. Best Regards, Bingbing ? Windows ????? ???: Axel Thielscher ????: 2022?6?13? 11:53 ???: ZHANG, bellabingbing [Student]; discuss at simnibs.org ??: Re: [Simnibs-discuss] ROI analysis using MNI coordinates using the middle cortical surfaces Hi, the fsaverage template is quite well aligned with MNI space. You can thus tryo to apply MNI coordinates and do the ROI analyses on the results mapped to fsaverage space. Best regards, Axel On 09-06-2022 16:31, ZHANG, bellabingbing [Student] wrote: Dear Madam or Sir, Hope this email finds you well. I am doing the TMS E-fields simulation. When I analysed the simulation results, I noticed we can use the default mesh file for ROI analysis using MNI coordinate or use middle cortical surfaces for ROI analysis based on atlas. However, I want to analyse the normal and tangent comments which are only stored in the middle cortical surfaces file. Can I use MNI coordinate for ROI analysis in this file? Looking forward to your reply! Best Regards, Bella [https://www.polyu.edu.hk/emaildisclaimer/85A-PolyU_Email_Signature.jpg] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information. _______________________________________________ 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/ [https://www.polyu.edu.hk/emaildisclaimer/85A-PolyU_Email_Signature.jpg] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information. -------------- next part -------------- An HTML attachment was scrubbed... URL: From benjamin.tessler at downstate.edu Mon Jun 20 19:05:42 2022 From: benjamin.tessler at downstate.edu (Benjamin Tessler) Date: Mon, 20 Jun 2022 17:05:42 +0000 Subject: [Simnibs-discuss] [EXTERNAL] Re: SimNibs simple volumes In-Reply-To: <32efe2dc-a83d-298f-541a-cc05a6f5319b@drcmr.dk> References: <32efe2dc-a83d-298f-541a-cc05a6f5319b@drcmr.dk> Message-ID: Hi Axel, Thank you for the response. I?m trying to learn how to import various volumes that I made in Autodesk, which exports STL and OBJ file formats. I can?t see any documentation on how to either import that into SimNIBS or convert it to nifti. It doesn?t import when I tried to convert it to a msh file from the gmsh software. Maybe is there a matlab script that can easily write nifti from an STL fomat? Best, Ben Sent from Mail for Windows From: Axel Thielscher Sent: Monday, June 13, 2022 5:57 AM To: Benjamin Tessler; discuss at simnibs.org Subject: [EXTERNAL] Re: [Simnibs-discuss] SimNibs simple volumes External email Do not click links, open attachments or provide your User ID or Password if the sender is unknown. Hi Benjamin, please try out simnibs 4 which is available as beta release. https://github.com/simnibs/simnibs/releases/tag/v4.0-beta1 It has new options to use custom-made meshes. After installation, click on index.html in the docs-folder to see the documentation for simnibs 4. Then follow the tutorial "How to create and use a custom mesh". Best, Axel On 08-06-2022 20:16, Benjamin Tessler wrote: Hi, I?m trying to just stimulate a block. What CAD do you recommend to use? I?m using Autodesk fusion 360 to make STL files. Then I use gmesh to make a msh file, but it won?t import into simnibs. Is there a simple way to make simple volumes? Best, Ben Sent from Mail for Windows The contents of this email message and any attachments are confidential and are intended solely for the addressee. The information may also be legally privileged. This transmission is sent in trust, for the sole purpose of delivery to the intended recipient. If you have received this transmission in error, any use, reproduction or dissemination of this transmission is strictly prohibited. If you are not the intended recipient, please immediately notify sender by reply email or by (718) 270-HELP. _______________________________________________ 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/ ________________________________ The contents of this email message and any attachments are confidential and are intended solely for the addressee. The information may also be legally privileged. This transmission is sent in trust, for the sole purpose of delivery to the intended recipient. If you have received this transmission in error, any use, reproduction or dissemination of this transmission is strictly prohibited. If you are not the intended recipient, please immediately notify sender by reply email or by (718) 270-HELP. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 057010908B3F4ECBAE0345BC6607E49E.png Type: image/png Size: 138 bytes Desc: 057010908B3F4ECBAE0345BC6607E49E.png URL: From oulap at drcmr.dk Tue Jun 21 09:43:03 2022 From: oulap at drcmr.dk (Oula) Date: Tue, 21 Jun 2022 09:43:03 +0200 Subject: [Simnibs-discuss] [EXTERNAL] Re: SimNibs simple volumes In-Reply-To: References: <32efe2dc-a83d-298f-541a-cc05a6f5319b@drcmr.dk> Message-ID: <9af98d24-fcd4-5dac-83d6-d01f3a15e2b6@drcmr.dk> Hi Ben, The files you created (at least the .stl) are surfaces. To use these in SimNIBS simulations you need volume meshes, i.e., tetrahedral meshes. I'm not familiar with .obj files, but you'd need to create volume meshes from the surfaces to import them into SimNIBS. To get started you can look at the .geo file that headreco generates. The name should be something like .geo. You can use that how to set up the .stl files to create a volume using gmsh. However, the surfaces need to be nested for that to work. Best, Oula On 6/20/22 19:05, Benjamin Tessler wrote: > > Hi Axel, > > Thank you for the response. I?m trying to learn how to import various > volumes that I made in Autodesk, which exports STL and OBJ file > formats. I can?t see any documentation on how to either import that > into SimNIBS or convert it to nifti. It doesn?t import when I tried to > convert it to a msh file from the gmsh software. Maybe is there a > matlab script that can easily write nifti from an STL fomat? > > Best, > > Ben > > Sent from Mail for > Windows > > *From: *Axel Thielscher > *Sent: *Monday, June 13, 2022 5:57 AM > *To: *Benjamin Tessler ; > discuss at simnibs.org > *Subject: *[EXTERNAL] Re: [Simnibs-discuss] SimNibs simple volumes > > External email > > /Do not click links, open attachments or provide your User ID or > Password if the sender is unknown./ > > Hi Benjamin, > > please try out simnibs 4 which is available as beta release. > > https://github.com/simnibs/simnibs/releases/tag/v4.0-beta1 > > > It has new options to use custom-made meshes. > > After installation, click on index.html in the docs-folder to see the > documentation for simnibs 4. Then follow the tutorial "How to create > and use a custom mesh". > > Best, > > Axel > > On 08-06-2022 20:16, Benjamin Tessler wrote: > > Hi, > > I?m trying to just stimulate a block. What CAD do you recommend to > use? I?m using Autodesk fusion 360 to make STL files. Then I use > gmesh to make a msh file, but it won?t import into simnibs. Is > there a simple way to make simple volumes? > > Best, > > Ben > > Sent from Mail > for Windows > > > The contents of this email message and any attachments are > confidential and are intended solely for the addressee. The > information may also be legally privileged. This transmission is > sent in trust, for the sole purpose of delivery to the intended > recipient. If you have received this transmission in error, any > use, reproduction or dissemination of this transmission is > strictly prohibited. If you are not the intended recipient, please > immediately notify sender by reply email or by (718) 270-HELP. > > _______________________________________________ > > 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/ > > > ------------------------------------------------------------------------ > > The contents of this email message and any attachments are > confidential and are intended solely for the addressee. The > information may also be legally privileged. This transmission is sent > in trust, for the sole purpose of delivery to the intended recipient. > If you have received this transmission in error, any use, reproduction > or dissemination of this transmission is strictly prohibited. If you > are not the intended recipient, please immediately notify sender by > reply email or by (718) 270-HELP. > > _______________________________________________ > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: 057010908B3F4ECBAE0345BC6607E49E.png Type: image/png Size: 138 bytes Desc: not available URL: From lmandersen at cfin.au.dk Wed Jun 22 13:34:35 2022 From: lmandersen at cfin.au.dk (=?utf-8?B?TGF1IE3DuGxsZXIgQW5kZXJzZW4=?=) Date: Wed, 22 Jun 2022 11:34:35 +0000 Subject: [Simnibs-discuss] Converting from .stl to .surf (freesurfer) Message-ID: <62e77733-7e16-f566-4af5-2c841e9a21b4@cfin.au.dk> Dear SimNIBS list Thank you for a great tool. I looked through the archive and couldn't find an answer for my question. I have used your headreco algorithm, and I created impressive looking renderings of the head and the brain of a subject. These are in the stl.format, and I was wondering whether there's a way to convert it to the .surf format found in FreeSurfer? Specifically, I need this to specify the boundaries between layers when specifying the BEM-model in MNE-Python. All the best wishes Lau M?ller Andersen -- Lau M?ller Andersen Ph.D. | Assistant Professor AIAS-COFUND Fellow (Aarhus Institute of Advanced Studies) aias.au.dk H?egh-Guldbergs Gade 6B 8000 Aarhus C Denmark & Department of Linguistics, Cognitive Science and Semiotics cognitive science School of Communication and Culture Faculty of Arts Aarhus University Building 1485, Room 524 Jens Christian Skous Vej 2 8000 Aarhus C Denmark & Center of Functionally Integrative Neuroscience cfin.au.dk Department of Clinical Medicine Faculty of Health Aarhus University Building 1710 Universitetsbyen 3 8000 Aarhus C Denmark Website: laumollerandersen.org Mail: lmandersen at cfin.au.dk and lmandersen at aias.au.dk GitHub: github.com/ualsbombe Twitter: twitter.com/ualsbombe Google Scholar: User Profile -------------- next part -------------- An HTML attachment was scrubbed... URL: From jesperdn at drcmr.dk Sat Jun 25 11:57:07 2022 From: jesperdn at drcmr.dk (Jesper Duemose Nielsen) Date: Sat, 25 Jun 2022 11:57:07 +0200 Subject: [Simnibs-discuss] Converting from .stl to .surf (freesurfer) In-Reply-To: <62e77733-7e16-f566-4af5-2c841e9a21b4@cfin.au.dk> References: <62e77733-7e16-f566-4af5-2c841e9a21b4@cfin.au.dk> Message-ID: <36d62bc0-3d18-671e-e42e-83a076d0796d@drcmr.dk> Hi Lau You could try something like this ---- from simnibs.msh.hmutils import mesh_load import mne fname_in = '/path/to/filename.stl' fname_out '/path/to/filename.surf' v, f = mesh_load(fname_in) # v, f = mne.surface.decimate_surface(v, f, n_triangles=5000) # or whatever mne.surface.write_surface(fname_out, v, f) ---- In my experience, the BEM implementation in MNE does not like the high density surfaces from simnibs so you may want to decimate them. I included a possible way of doing it. Best, Jesper On 6/22/2022 13:34, Lau M?ller Andersen wrote: > > Dear SimNIBS list > > Thank you for a great tool. > > I looked through the archive and couldn't find an answer for my > question. I have used your headreco algorithm, and I created > impressive looking renderings of the head and the brain of a subject. > These are in the stl.format, and I was wondering whether there's a way > to convert it to the .surf format found in FreeSurfer? > > Specifically, I need this to specify the boundaries between layers > when specifying the BEM-model in MNE-Python. > > All the best wishes > > Lau M?ller Andersen > > -- > Lau M?ller Andersen > Ph.D. | Assistant Professor > > AIAS-COFUND Fellow (Aarhus Institute of Advanced Studies) aias.au.dk > H?egh-Guldbergs Gade 6B > 8000 Aarhus C > Denmark > & > Department of Linguistics, Cognitive Science and Semiotics cognitive > science > School of Communication and Culture > Faculty of Arts > Aarhus University > Building 1485, Room 524 > Jens Christian Skous Vej 2 > 8000 Aarhus C > Denmark > & > Center of Functionally Integrative Neuroscience cfin.au.dk > Department of Clinical Medicine > Faculty of Health > Aarhus University > Building 1710 > Universitetsbyen 3 > 8000 Aarhus C > Denmark > > Website: laumollerandersen.org > Mail: lmandersen at cfin.au.dk and lmandersen at aias.au.dk > GitHub: github.com/ualsbombe > Twitter: twitter.com/ualsbombe > Google Scholar: User Profile > > > _______________________________________________ > 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 m.lueckel at yahoo.de Wed Jun 29 13:14:33 2022 From: m.lueckel at yahoo.de (=?UTF-8?Q?Maximilian_L=C3=BCckel?=) Date: Wed, 29 Jun 2022 11:14:33 +0000 (UTC) Subject: [Simnibs-discuss] Diffusion tensor information ignored References: <1947686326.2098614.1656501273258.ref@mail.yahoo.com> Message-ID: <1947686326.2098614.1656501273258@mail.yahoo.com> Hi, whenever I run simulations using a python script, the diffusion tensor information in d2c_subID/dti_results_T1space/DTI_conf_tensor.nii.gz is being ignored, stating that "isotropic conductivities" are used. This is even the case when explicitly specifying the path to the NifTi file with conductivity tensors in s.fname_tensor. Any idea why that is? Thanks, Max -------------- next part -------------- An HTML attachment was scrubbed... URL: