From Morgan.Thienpont at UGent.be Wed Nov 3 15:00:26 2021 From: Morgan.Thienpont at UGent.be (Morgan Thienpont) Date: Wed, 3 Nov 2021 14:00:26 +0000 Subject: [Simnibs-discuss] question about projection Message-ID: Dear I sent this email with the following question: Is there a possible function in matlab to find the coordinates of the rTMS coil after the coordinates of the ROI are projected on the scalp? Kinds regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From victoria.shevchenko at ens.psl.eu Mon Nov 15 12:47:09 2021 From: victoria.shevchenko at ens.psl.eu (Victoria Shevchenko) Date: Mon, 15 Nov 2021 12:47:09 +0100 Subject: [Simnibs-discuss] Reference electrode at right deltoid Message-ID: <4A23AB1C-DD95-477F-A588-550DB6E5072E@ens.psl.eu> Hello, I am currently generating tDCS simulations of different montages and one of them involves a cathode on the right deltoid muscle. Does SimNIBS allow for this electrode placement? Thanks so much in advance. Best regards, Victoria SHEVCHENKO From zhen.li.dada at gmail.com Sun Nov 21 18:24:59 2021 From: zhen.li.dada at gmail.com (Zhen Li) Date: Sun, 21 Nov 2021 18:24:59 +0100 Subject: [Simnibs-discuss] mri2mesh mri_convert Message-ID: Dear researchers, I used SimNIBS to build head model, and there was a error like this: mri2mesh --all ernie2 org/ernie2_T1.nii.gz org/ernie2_T2.nii.gz Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/bash_modules/mri2mesh: line 107:mri_convert: command not found exiting mri2mesh after error Could you help me with this error? Thank you in advance. Zhen -------------- next part -------------- An HTML attachment was scrubbed... URL: From zhen.li.dada at gmail.com Fri Nov 26 10:24:28 2021 From: zhen.li.dada at gmail.com (Zhen Li) Date: Fri, 26 Nov 2021 10:24:28 +0100 Subject: [Simnibs-discuss] dwi2cond Message-ID: Dear researchers, When I run codes to prepare DTI images in SimNIBS on Mac: dwi2cond --all --eddy --phasedir=-y --readout=0.05 ernie org/ernie_dMRI.nii.gz org/ernie_dMRI.bval org/ernie_dMRI.bvec org/ernie_dMRI_rev.nii.gz The error shows mainly like this: *eddy: msg=--rep_ol cannot be used for this version of eddy* but for the given patch here : https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Patches, there is no other version as its recommendation:* e.g. 5.0.0 to 5.0.2* I can only download *5.0.9 to 5.0.X or **5.0.9 to 5.0.8*. I am not sure if it is to do with the version issue. Could you please help me with that? I appreciate it?. Best regards, Zhen -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Fri Nov 26 13:46:42 2021 From: axelt at drcmr.dk (Axel Thielscher) Date: Fri, 26 Nov 2021 13:46:42 +0100 Subject: [Simnibs-discuss] dwi2cond In-Reply-To: References: Message-ID: <70420f52-7b98-f734-a895-9e4f056988cd@drcmr.dk> Hi, please open the file "dwi2cond", which is in the simnibs/bash_modules subfolder of your simnibs installation and change (around line 56) EDDYOPT='--repol' to EDDYOPT='' Best regards, Axel On 11/26/2021 10:24 AM, Zhen Li wrote: > Dear researchers, > > When I run codes to prepare DTI images in SimNIBS on Mac: > > dwi2cond --all --eddy --phasedir=-y --readout=0.05 ernie > org/ernie_dMRI.nii.gz org/ernie_dMRI.bval org/ernie_dMRI.bvec > org/ernie_dMRI_rev.nii.gz > > The error shows mainly like this: > > *eddy: msg=--rep_ol cannot be used for this version of eddy* > > but for the given patch here : > https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Patches, > there is no other version as its recommendation:*e.g. 5.0.0 to 5.0.2* > I can only download *5.0.9 to 5.0.X or **5.0.9 to 5.0.8*. > > I am not sure if it is to do with the version issue. > Could you please help me with?that? > I appreciate it?. > > Best regards, > Zhen > > _______________________________________________ > 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 brunommansur at gmail.com Sat Nov 27 23:41:33 2021 From: brunommansur at gmail.com (Bruno Mansur) Date: Sat, 27 Nov 2021 23:41:33 +0100 Subject: [Simnibs-discuss] Ernie as a model Message-ID: Dear Simnibs community, I'm new to current flow modeling and I would like to run an optimization for a brain stimulation study. Would you recommend me to use the subject "Ernie" from the example dataset? I haven't found any publications using it. Best, Bruno -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Mon Nov 29 15:09:50 2021 From: axelt at drcmr.dk (Axel Thielscher) Date: Mon, 29 Nov 2021 15:09:50 +0100 Subject: [Simnibs-discuss] Ernie as a model In-Reply-To: References: Message-ID: <2c24fb9b-6844-3fb4-ab33-d995698ba380@drcmr.dk> Hi Bruno, the ernie model should be fine as a starting point. You can consider repeating the simulations on several head models to see how stable the resulting fields of your optimized montage are. Best regards, Axel On 11/27/2021 11:41 PM, Bruno Mansur wrote: > Dear Simnibs community, > > I'm new to current flow modeling and I would like to run an > optimization for a brain stimulation study. Would you recommend me to > use the subject "Ernie" from the example dataset? I haven't found any > publications using it. > > Best, > > Bruno > > _______________________________________________ > 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 lucia.bulubas at med.uni-muenchen.de Tue Nov 30 16:27:14 2021 From: lucia.bulubas at med.uni-muenchen.de (Lucia Bulubas) Date: Tue, 30 Nov 2021 16:27:14 +0100 Subject: [Simnibs-discuss] Mag&More PMD70 Coil file Message-ID: <582FA8B6-4852-433D-9944-595A3FB375E9@med.uni-muenchen.de> Dear Simnibs Discuss group, We are looking to simulate TMS using the PMD70 coil from Mag&More, is there a coil file available or can you recommend which coil file to use instead? Thank you very much! Dr. med. Lucia Bulubas Assistenz?rztin, PhD cand. Leitung Stimulations-Ambulanz, Munich Center for Brain Stimulation MR-informed neurostimulation (The MiNK lab) LMU Klinikum Klinik f?r Psychiatrie und Psychotherapie Tel. 089 4400-55821 | Fax 089 4400-55890 International Max Planck Research School for Translational Psychiatry (IMPRS-TP) -------------- next part -------------- An HTML attachment was scrubbed... URL: