From giacomo.bertazzoli at unitn.it Fri Jul 2 17:12:27 2021 From: giacomo.bertazzoli at unitn.it (Giacomo Bertazzoli) Date: Fri, 2 Jul 2021 17:12:27 +0200 Subject: [Simnibs-discuss] TMS coil visualization Message-ID: Dear all, I am trying to figure out the meaning of the green "L" shaped representation of the TMS coil in the output of a basic TMS simNIBS simulation. What does the long part represent? The cortex to coil distance? And the small ortogonal leg of the "L" is pointing towards the handle of the coil? Or is it the direction of the current flowing in the coil? I did not find this information on the website, I already apologize if I just missed it. I am including a screenshot down here hoping it could be visualized. All the very best! Giacomo Bertazzoli [image: image.png] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 1337703 bytes Desc: not available URL: From maxime.janbon1 at outlook.com Wed Jul 7 18:29:12 2021 From: maxime.janbon1 at outlook.com (Maxime Janbon) Date: Wed, 7 Jul 2021 16:29:12 +0000 Subject: [Simnibs-discuss] Problems with headreco Message-ID: Dear Sir/Madam, I am contacting you on behalf of Antonio Valerio Cabre?s laboratory in Paris. We are running into an issue creating head models using the headreco package. When using it in the command line of the terminal, we receive the error message: Bash: command not found We have tried using this command to: 1. Construct head models from the Ernie example dataset 2. Using our own MRIs and 3. Reconstructing head models after having corrected some segmentations. In all three cases, the same error message was received. We are using the 2018 version of Matlab on an iMac running macOS Mojave (version 10.14.5). Matlab is installed, running and has been added to the path. We have also installed SimNibs, although the we have also encountered problems opening the SimNibs GUI. Many thanks for any advice. Best regards, Maxime Janbon -------------- next part -------------- An HTML attachment was scrubbed... URL: From DXA869 at student.bham.ac.uk Thu Jul 8 16:53:54 2021 From: DXA869 at student.bham.ac.uk (DXA869 at student.bham.ac.uk) Date: Thu, 8 Jul 2021 14:53:54 +0000 Subject: [Simnibs-discuss] Which template to use and why? Message-ID: <0710e91329124a20b76b2fbd24d08ada@student.bham.ac.uk> Hi, I used both ERNIE and MNI as templates for my simulations however, I was wondering what is the rationale behind the choice of ERNIE over MNI. I made some simulations of the current spread with an M1-tDCS setup and I can't decide which simulation I should include in the paper I am working on. MNI looks a bit easier to understand in terms of neuroanatomy. Best, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From alberto.benelli at stud.unifi.it Fri Jul 9 17:33:54 2021 From: alberto.benelli at stud.unifi.it (Alberto Benelli) Date: Fri, 9 Jul 2021 17:33:54 +0200 Subject: [Simnibs-discuss] Upload MR scans Message-ID: <272EA04C-3FEA-42E7-A031-9F3BBD0BF71F@gmail.com> Hi, I am using simnibs to do simulations on healthy subjects for electrical stimulation. These subjects have previously had a structural MRI scan. How can I insert these scans in order to create individualised stimulation simulations on each subject? Is it possible to upload subject's MRI? Thanks, Alberto From kristofferm at drcmr.dk Tue Jul 13 10:45:15 2021 From: kristofferm at drcmr.dk (Kristoffer Madsen) Date: Tue, 13 Jul 2021 10:45:15 +0200 Subject: [Simnibs-discuss] TMS coil visualization In-Reply-To: References: Message-ID: Hi Giacomo, The long part just represents the z-direction of the coil, the length of it is just constant. The other leg of the L points in the positive y-direction of the coil - exactly what this means depends on the coil, but for most figure-of-eight coils this is the opposite direction of the handle (some coils have the handle pointing in the negative z-direction). Best, Kristoffer On Sun, 11 Jul 2021 at 20:43, Giacomo Bertazzoli < giacomo.bertazzoli at unitn.it> wrote: > Dear all, > I am trying to figure out the meaning of the green "L" shaped > representation of the TMS coil in the output of a basic TMS simNIBS > simulation. What does the long part represent? The cortex to coil distance? > And the small ortogonal leg of the "L" is pointing towards the handle of > the coil? Or is it the direction of the current flowing in the coil? > I did not find this information on the website, I already apologize if I > just missed it. > I am including a screenshot down here hoping it could be visualized. > All the very best! > > Giacomo Bertazzoli > [image: image.png] > _______________________________________________ > 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: image.png Type: image/png Size: 1337703 bytes Desc: not available URL: From giacomo.bertazzoli at unitn.it Fri Jul 16 18:48:24 2021 From: giacomo.bertazzoli at unitn.it (Giacomo Bertazzoli) Date: Fri, 16 Jul 2021 18:48:24 +0200 Subject: [Simnibs-discuss] TMS optimization Message-ID: Dear all, I am facing the problem of comparing the coil orientation extracted after an e-field simulation (position matrix in the log file) with the coil orientation suggested after the TMS optimization procedure available on simNIBS. However I noticed a discrepancy between the coil center projected by simNIBS during the e-field simulation (simNIBS infers the coil center automatically when I input a cortical target) and the one given as final output by the TMS optimization, even if I provide as input both the coil center and the cortical target. What I am trying to obtain from the TMS optimization is a position matrix that has the last column (coil center) identical to the one I get after the e-field simulation. Has someone already faced this problem? Do you have any suggestions? Thank you for your great support, All the very best, Giacomo -- Giacomo Bertazzoli, PhD Candidate Cognition Neurostimulation & Connectivity Lab - CIMeC University of Trento, Corso Bettini 31, 38068 Rovereto (TN) Italy Email: giacomo.bertazzoli at unitn.it https://webapps.unitn.it/du/en/Persona/PER0194098 https://www.linkedin.com/in/giacomo-bertazzoli-8737b160/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stein at uq.edu.au Sat Jul 17 09:11:06 2021 From: a.stein at uq.edu.au (Athena Stein) Date: Sat, 17 Jul 2021 07:11:06 +0000 Subject: [Simnibs-discuss] Scripting headreco Message-ID: Hi, I am interested in doing a group-level analysis of subjects (as discussed in Advanced Features). I am wondering if there is any way to script the headreco command, or a faster way to make several (i.e. around 90) head models? If anyone has already written a script and is willing to share, please let me know! Kind regards, Athena Athena Stein MPH BBiomedSc PhD Student Casual Academic UQ Child Health Research Centre Acquired Brain Injury in Children research program (ABiC) Centre for Children's Health Research Level 6, 62 Graham St South Brisbane Qld 4101 Australia T +61 7 3069 7555 E a.stein at uq.edu.au W child-health-research.centre.uq.edu.au CRICOS 00025B [cid:image001.png at 01D77B2E.BA569EF0] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 93663 bytes Desc: image001.png URL: From axelt at drcmr.dk Tue Jul 27 16:18:30 2021 From: axelt at drcmr.dk (Axel Thielscher) Date: Tue, 27 Jul 2021 16:18:30 +0200 Subject: [Simnibs-discuss] TMS optimization In-Reply-To: References: Message-ID: <8ead4a84-ea55-ee42-7ef9-701eee0e705c@drcmr.dk> Dear Giacomo, to make sure we understand correctly: You only? want to optimize the coil orientation, but keep the center position fixed? How different is the last column? Small shifts can occur because the position is aligned to the closest skin node at some parts of the code (we will change this behavoir at some point in the future). Best regards, Axel On 7/16/2021 6:48 PM, Giacomo Bertazzoli wrote: > Dear all, > I am facing the problem of comparing the coil orientation extracted > after an e-field simulation (position matrix in the log file) with the > coil orientation suggested after the TMS optimization procedure > available on simNIBS. However I noticed a discrepancy between the coil > center projected by simNIBS during the e-field simulation (simNIBS > infers the coil center automatically when I input a cortical target) > and the one given as final output by the TMS optimization, even if I > provide as input both the coil center and the cortical target. > > What I am trying to obtain from the TMS optimization?is a > position?matrix that has the last column (coil center) identical to > the one I get after the e-field simulation. > Has someone already faced this problem? Do you have any suggestions? > Thank you for your great support, > All?the very best, > > Giacomo > > -- > Giacomo Bertazzoli, PhD Candidate > Cognition Neurostimulation & Connectivity Lab - CIMeC > University of Trento, Corso Bettini 31, 38068 Rovereto (TN) Italy > Email: giacomo.bertazzoli at unitn.it > https://webapps.unitn.it/du/en/Persona/PER0194098 > > https://www.linkedin.com/in/giacomo-bertazzoli-8737b160/ > > > _______________________________________________ > 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: