From gh.soleimani_70 at yahoo.com Wed Oct 7 20:43:23 2020 From: gh.soleimani_70 at yahoo.com (Ghazale Soleimani) Date: Wed, 7 Oct 2020 18:43:23 +0000 (UTC) Subject: [Simnibs-discuss] Area under electrode References: <247581136.610825.1602096203093.ref@mail.yahoo.com> Message-ID: <247581136.610825.1602096203093@mail.yahoo.com> Dear SimNIBS team, I have a question about the area under the electrode. For example, I have placed an electrode (circular pad or rectangular) in F3 over the scalp in EEG standard system. I want to find the area under the electrode over the gray matter both in MNI space and subject-specific space. Do you have any suggestions? Stay healthy,Ghazaleh -------------- next part -------------- An HTML attachment was scrubbed... URL: From gh.soleimani_70 at yahoo.com Thu Oct 8 08:36:25 2020 From: gh.soleimani_70 at yahoo.com (Ghazale Soleimani) Date: Thu, 8 Oct 2020 06:36:25 +0000 (UTC) Subject: [Simnibs-discuss] Fw: Area under electrode In-Reply-To: <247581136.610825.1602096203093@mail.yahoo.com> References: <247581136.610825.1602096203093.ref@mail.yahoo.com> <247581136.610825.1602096203093@mail.yahoo.com> Message-ID: <904000539.770698.1602138985852@mail.yahoo.com> Dear Dr Thielscher,Dear SimNIBS team, Many thanks for your great software :) I have a question about the area under the electrode. For example, I have placed an electrode (circular pad or rectangular) in F3 over the scalp in EEG standard system. I want to find the area under the electrode over the gray matter both in MNI space and subject-specific space. Do you have any suggestions? Stay healthy,Ghazaleh -------------- next part -------------- An HTML attachment was scrubbed... URL: From sepidehkhaksar123 at gmail.com Mon Oct 12 19:16:08 2020 From: sepidehkhaksar123 at gmail.com (sepideh khaksar) Date: Mon, 12 Oct 2020 20:46:08 +0330 Subject: [Simnibs-discuss] Probably something went wrong with the Matlab call or SPM Message-ID: hi Although MATLAB is installed, I get the following error when I use Headerco on Linux headreco all --cat ernie org/ernie_T1.nii.gz org/ernie_T2.nii.gz ======================================================================== PREPARING VOLUMES FOR MESHING ======================================================================== Copying input files to m2m_ernie Copying T1fs.nii.gz to T1fs_conform.nii.gz Preparing to segment Starting MATLAB ======================================================================== Binarizing tissue probability maps Traceback (most recent call last): File "/home/sepideh/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 13, in main() File "/home/sepideh/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main headmodel(sys.argv) File "/home/sepideh/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 265, in headmodel raise OSError('Could not find tissue probability maps.\n' OSError: Could not find tissue probability maps. Probably something went wrong with the Matlab call or SPM What is the problem? Thank you for your help -------------- next part -------------- An HTML attachment was scrubbed... URL: From mccalled at musc.edu Tue Oct 13 19:11:08 2020 From: mccalled at musc.edu (Mccalley, Daniel) Date: Tue, 13 Oct 2020 17:11:08 +0000 Subject: [Simnibs-discuss] Method for assessing STC distance Message-ID: Hi all, I was wondering if you could share a little more information about how SIMNIBs calculates scalp-to-cortex distance (perhaps this is published somewhere?). Is the measurement made by calculating the shortest distance from the EEG site to the outermost point of the cortex? Or perhaps it's the distance from the EEG site to the deepest sulcus? I've calculated this distance at FP1 by hand a few times and my hand measurements seem to be quite different than the automatic SIMNIBs output so I'm trying to learn more about why these measurement are so different. Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience -------------- next part -------------- An HTML attachment was scrubbed... URL: From elisabeth.kaminski at uni-leipzig.de Wed Oct 14 09:22:47 2020 From: elisabeth.kaminski at uni-leipzig.de (Elisabeth Kaminski) Date: Wed, 14 Oct 2020 09:22:47 +0200 Subject: [Simnibs-discuss] head mesh oder adult Message-ID: <20201014092247.Horde.po_Ve7Yb2q9LZhJcmbj-NW3@mail.uni-leipzig.de> Dear SIMNIBS community, is anyone aware of a head mesh comparable to Ernie from an older subject? A reviewer asked for tDCS-simulation of an older adult but unfortunately we did not include MRI measurements in our research design. Thank you in advance Elisabeth From oupu at dtu.dk Mon Oct 19 08:28:49 2020 From: oupu at dtu.dk (Oula Puonti) Date: Mon, 19 Oct 2020 06:28:49 +0000 Subject: [Simnibs-discuss] Method for assessing STC distance In-Reply-To: References: Message-ID: <6b09a1a2d6b949b1affee3534d693c2d@dtu.dk> Hi Dan, It's actually the coil-to-cortex distance that SimNIBS writes out. The distance is calculated from the center of the coil to the closest point on the cortex. If you want to calculate the scalp-to-cortex distance you can just set the coil to head surface distance to zero in the simulations. Best, Oula ________________________________ From: Simnibs-discuss on behalf of Mccalley, Daniel Sent: Tuesday, October 13, 2020 7:11:08 PM To: discuss at simnibs.org Subject: [Simnibs-discuss] Method for assessing STC distance Hi all, I was wondering if you could share a little more information about how SIMNIBs calculates scalp-to-cortex distance (perhaps this is published somewhere?). Is the measurement made by calculating the shortest distance from the EEG site to the outermost point of the cortex? Or perhaps it's the distance from the EEG site to the deepest sulcus? I've calculated this distance at FP1 by hand a few times and my hand measurements seem to be quite different than the automatic SIMNIBs output so I'm trying to learn more about why these measurement are so different. Best, Dan McCalley Medical University of South Carolina College of Graduate Studies, Neuroscience -------------- next part -------------- An HTML attachment was scrubbed... URL: From sybren.vanhoornweder at uhasselt.be Sat Oct 17 13:39:08 2020 From: sybren.vanhoornweder at uhasselt.be (Sybren VAN HOORNWEDER) Date: Sat, 17 Oct 2020 13:39:08 +0200 Subject: [Simnibs-discuss] center surround montage in tACS Message-ID: <8A930AAE-97B3-4062-978B-BDBF57DEF92D@hxcore.ol> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: FF22404631FE49FB96744A72CAAE1F0B[6303091].jpg Type: image/jpeg Size: 5352 bytes Desc: not available URL: From oupu at dtu.dk Tue Oct 20 16:08:57 2020 From: oupu at dtu.dk (Oula Puonti) Date: Tue, 20 Oct 2020 14:08:57 +0000 Subject: [Simnibs-discuss] Probably something went wrong with the Matlab call or SPM In-Reply-To: References: Message-ID: Hi, Seems you're using simnibs version 3.2. In this case --cat should be the default option. Can you try running without that flag? If it still fails in the same place, please try installing the newest version of SimNIBS. Best, Oula ________________________________ From: Simnibs-discuss on behalf of sepideh khaksar Sent: Monday, October 12, 2020 7:16:08 PM To: discuss at simnibs.org Subject: [Simnibs-discuss] Probably something went wrong with the Matlab call or SPM hi Although MATLAB is installed, I get the following error when I use Headerco on Linux headreco all --cat ernie org/ernie_T1.nii.gz org/ernie_T2.nii.gz ======================================================================== PREPARING VOLUMES FOR MESHING ======================================================================== Copying input files to m2m_ernie Copying T1fs.nii.gz to T1fs_conform.nii.gz Preparing to segment Starting MATLAB ======================================================================== Binarizing tissue probability maps Traceback (most recent call last): File "/home/sepideh/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 13, in main() File "/home/sepideh/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main headmodel(sys.argv) File "/home/sepideh/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 265, in headmodel raise OSError('Could not find tissue probability maps.\n' OSError: Could not find tissue probability maps. Probably something went wrong with the Matlab call or SPM What is the problem? Thank you for your help -------------- next part -------------- An HTML attachment was scrubbed... URL: From bld58 at drexel.edu Tue Oct 20 16:31:06 2020 From: bld58 at drexel.edu (Deck,Benjamin) Date: Tue, 20 Oct 2020 14:31:06 +0000 Subject: [Simnibs-discuss] Geodesic distance between stimulation sites Message-ID: Hello, I am attempting to calculate geodesic distance across the cortex between two TMS simulation locations. Is there a tool within the Simnibs package that is able to perform this operation? Ben -------------- next part -------------- An HTML attachment was scrubbed... URL: From oupu at dtu.dk Fri Oct 23 08:20:21 2020 From: oupu at dtu.dk (Oula Puonti) Date: Fri, 23 Oct 2020 06:20:21 +0000 Subject: [Simnibs-discuss] Geodesic distance between stimulation sites In-Reply-To: References: Message-ID: <7ac35fad19f647d28b915a870b635071@dtu.dk> Hi Ben, We don't have a function for calculating the geodesic distance, but I found this python package: https://github.com/NeuroanatomyAndConnectivity/surfdist which takes in triangular surfaces and calculates the geodesic distance between two locations. For the calculation it relies on this package: https://pypi.org/project/gdist/ You can probably feed in the central gray matter surface to one of the packages above and get the distance out. Best, Oula ________________________________ From: Simnibs-discuss on behalf of Deck,Benjamin Sent: Tuesday, October 20, 2020 4:31:06 PM To: discuss at simnibs.org Subject: [Simnibs-discuss] Geodesic distance between stimulation sites Hello, I am attempting to calculate geodesic distance across the cortex between two TMS simulation locations. Is there a tool within the Simnibs package that is able to perform this operation? Ben -------------- next part -------------- An HTML attachment was scrubbed... URL: From oupu at dtu.dk Fri Oct 23 13:57:31 2020 From: oupu at dtu.dk (Oula Puonti) Date: Fri, 23 Oct 2020 11:57:31 +0000 Subject: [Simnibs-discuss] head mesh oder adult In-Reply-To: <20201014092247.Horde.po_Ve7Yb2q9LZhJcmbj-NW3@mail.uni-leipzig.de> References: <20201014092247.Horde.po_Ve7Yb2q9LZhJcmbj-NW3@mail.uni-leipzig.de> Message-ID: <1d6b60a3ec6941c3a6ca3e8bafd0141b@dtu.dk> Hi Elisabeth, Not sure how old subject you're looking for, but we have a set of open source head models available here: https://osf.io/exbd5/ Subject "sub-control18" is a 59 year old male. Would that fit the bill? Otherwise if you can find a scan of a suitable subject from some open-source data repository you could run that through SimNIBS. Best, Oula ________________________________ From: Simnibs-discuss on behalf of Elisabeth Kaminski Sent: Wednesday, October 14, 2020 9:22:47 AM To: discuss at simnibs.org Subject: [Simnibs-discuss] head mesh oder adult Dear SIMNIBS community, is anyone aware of a head mesh comparable to Ernie from an older subject? A reviewer asked for tDCS-simulation of an older adult but unfortunately we did not include MRI measurements in our research design. Thank you in advance Elisabeth _______________________________________________ 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 oupu at dtu.dk Mon Oct 26 11:16:17 2020 From: oupu at dtu.dk (Oula Puonti) Date: Mon, 26 Oct 2020 10:16:17 +0000 Subject: [Simnibs-discuss] center surround montage in tACS In-Reply-To: <8A930AAE-97B3-4062-978B-BDBF57DEF92D@hxcore.ol> References: <8A930AAE-97B3-4062-978B-BDBF57DEF92D@hxcore.ol> Message-ID: Hi Sybren, For some reason I can't see the attachment, but you can see how to set-up the center-surround montage here: https://github.com/simnibs/simnibs/blob/master/simnibs/examples/simulations/tDCS_ring.py Best, Oula ________________________________ From: Simnibs-discuss on behalf of Sybren VAN HOORNWEDER Sent: Saturday, October 17, 2020 1:39:08 PM To: discuss at simnibs.org Subject: [Simnibs-discuss] center surround montage in tACS I?m Sybren, PhD student at UHasselt. I?ve been using SimNIBS (3.2.1) for modeling the induced electrical fields from dsTMS paradigms. Now, for my PhD, I?m looking into the effects of tACS and would like to use SimNIBS for this as well. When reading the paper of Saturnino et al. (2017); ?How to target inter-regional phase synchronisation with dual-site tACS? I saw that it was possible to simulate the induced electrical field from a center-surround montage. This is the same montage that I?m using but I can?t seem to find how to create the open, outer rings. I?m stuck with two outer electrodes at each location, both without an opening (see attachment). I contacted drs. Saturnino regarding this but he mentioned I should rather contact you instead. Is there a option in the GUI to enable this or are there any forums that share scripts to do so? Thank you for the amazing software, it is truly useful for my research! With kind regards Sybren Van Hoornweder PhD student www.uhasselt.be Universiteit Hasselt - Campus Diepenbeek Agoralaan Gebouw A - B-3590 Diepenbeek Kantoor Kantoor A1.04 [cid:image001.jpg at 01D697E7.58B08010] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: FF22404631FE49FB96744A72CAAE1F0B[6303091].jpg Type: image/jpeg Size: 5352 bytes Desc: FF22404631FE49FB96744A72CAAE1F0B[6303091].jpg URL: From elisabeth.kaminski at uni-leipzig.de Mon Oct 26 08:28:58 2020 From: elisabeth.kaminski at uni-leipzig.de (Dr. Elisabeth Kaminski) Date: Mon, 26 Oct 2020 08:28:58 +0100 Subject: [Simnibs-discuss] head mesh oder adult In-Reply-To: <1d6b60a3ec6941c3a6ca3e8bafd0141b@dtu.dk> References: <20201014092247.Horde.po_Ve7Yb2q9LZhJcmbj-NW3@mail.uni-leipzig.de> <1d6b60a3ec6941c3a6ca3e8bafd0141b@dtu.dk> Message-ID: Dear Oula, thanks a lot for your suggestion! I will have a look at the os head models! CHeers Elisabeth Am 23.10.2020 um 13:57 schrieb Oula Puonti: > > Hi Elisabeth, > > > Not sure how old subject you're looking for, but we have a set of open > source head models available here: > > > https://osf.io/exbd5/ > > Subject "sub-control18" is a 59 year old male. Would that fit the > bill? Otherwise if you can find a scan of a?suitable subject from some > open-source data repository you could run that through SimNIBS. > > > Best, > Oula > > ------------------------------------------------------------------------ > *From:* Simnibs-discuss on behalf > of Elisabeth Kaminski > *Sent:* Wednesday, October 14, 2020 9:22:47 AM > *To:* discuss at simnibs.org > *Subject:* [Simnibs-discuss] head mesh oder adult > Dear SIMNIBS community, > > is anyone aware of a head mesh comparable to Ernie from an older > subject? A reviewer asked for tDCS-simulation of an older adult but > unfortunately we did not include MRI measurements in our research > design. > > Thank you in advance > Elisabeth > > > _______________________________________________ > Simnibs-discuss mailing list > Simnibs-discuss at drcmr.dk > https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss -- Dr. ELisabeth Kaminski Akademische Assistentin Universit?t Leipzig Sportwissenschaftliche Fakult?t Institut f?r allgemeine Bewegungs- und Trainingswissenschaften Jahnallee 59, 04109 Leipzig T +49 341 97-31686 F +49 341 97-31679 elisabeth.kaminski(at)uni-leipzig.de http://www.spowi.uni-leipzig.de/fakultaet/institute-fachgebiete/abtw/personal/kaminski/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From Vighneshvel.Thiruppathi at lin-magdeburg.de Thu Oct 29 12:35:22 2020 From: Vighneshvel.Thiruppathi at lin-magdeburg.de (Vighneshvel Thiruppathi) Date: Thu, 29 Oct 2020 11:35:22 +0000 Subject: [Simnibs-discuss] Modelling iDCMS Message-ID: <93CF86BA-5598-4C19-B028-68DF497E2F18@lin-magdeburg.de> Dear simNIBS, My name is Vighnesh and I am a graduate student at Prof. Michael Brosch?s lab. We have been working on intracranial direct current macrostimulation (iDCMS) in macaque auditory cortex and were wondering if we could model the spatial spread of DC-induced electric field. I found tutorials on TMS & tDCS in your website but couldn?t find anything on iDCMS. Could you please let me know if we can model iDCMS? If so, how? Any assistance is highly appreciated. Looking forward to your email! Regards, Vighnesh. -- Vighnesh Thiruppathi, Primate Neurobiology Lab, Leibniz Institute for Neurobiology, 39118 ? Magdeburg. 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