From hkim17 at korea.ac.kr Fri Jul 1 06:39:31 2022 From: hkim17 at korea.ac.kr (=?UTF-8?B?4oCN6rmA7ZiV6recWyDqtZDsiJggLyDrh4zqs7XtlZnsl7DqtazshowgXQ==?=) Date: Fri, 1 Jul 2022 13:39:31 +0900 Subject: [Simnibs-discuss] Using Captrak coordinates for the optimization Message-ID: To whom it may concern, Hello, I am Hyoungkyu Kim, a research professor in the brain engineering department at Korea University. First of all, I really appreciate using your great program, SimNIBS, for my research. The completion of the program is amazing and the tutorials are easy to understand. Our team is planning to measure EEG and fMRI during the memory task (sternberg test) under the tES stimulation, and I think SimNIBS is a perfect solution to optimize the stimulation by using a personal T1 image. I checked I can use personalized coordinates in the calculation of the leadfield, and I have the coordinates of Captrak ( https://brainvision.com/products/captrak/). *I wonder if I can have the codes or information transforming Captrak coordinates to MNI coordinates (or to other coordinates) because I have not much experience with the registration between two different coordinates properly. * It will be really helpful to me if I can have any advice from you. Thank you so much and have a great day! Best, Hyoungkyu Kim -------------- next part -------------- An HTML attachment was scrubbed... URL: From marton at stud.uni-heidelberg.de Fri Jul 1 10:46:16 2022 From: marton at stud.uni-heidelberg.de (Jens Marton) Date: Fri, 1 Jul 2022 10:46:16 +0200 Subject: [Simnibs-discuss] Example dataset resolution Message-ID: Dear everyone, I'm Jens, a computer science student from Heidelberg, Germany. I've been wondering if "Ernie" from the example dataset exists somewhere in a higher resolution, or - if not - if anyone knows of a (free to use) head model with a higher reslution than Ernie. Kind regards Jens Marton From utkarshpancholi6387 at gmail.com Fri Jul 1 12:19:41 2022 From: utkarshpancholi6387 at gmail.com (Utkarsh Pancholi) Date: Fri, 1 Jul 2022 15:49:41 +0530 Subject: [Simnibs-discuss] Measurement of tissue volume in region of interest Message-ID: Dear sir, I wanted to know how I can measure a volume of a specific region in a brain using SimNIBS pipeline. For example, I want to know the total volume of the entorhinal cortex or left hippocampus. So I can relate to the volume and electric field strength relationship in multiple subjects. It would be a great help if you can guide in this regard. ----------------------------------------------------------------------------------------------------- UTKARSH V. PANCHOLI ASSISTANT PROFESSOR BIOMEDICAL ENGINEERING L.D COLLEGE OF ENGINEERING AHMEDABAD-380015 -------------- next part -------------- An HTML attachment was scrubbed... URL: From axelt at drcmr.dk Fri Jul 1 18:07:22 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Fri, 1 Jul 2022 18:07:22 +0200 Subject: [Simnibs-discuss] Example dataset resolution In-Reply-To: References: Message-ID: <205faf59-2de0-2cfa-eb69-3e7c863a6ead@drcmr.dk> Hi Jens, when your question regards the resolution of the MR images: no, there are no higher resolution versions. In case your question is related to the mesh resolution: Just recreate it at the resolution you need. You can control the mesh resolution using the -v option in headreco, see https://simnibs.github.io/simnibs/build/html/documentation/command_line/headreco.html for how to do that. Best, Axel On 01-07-2022 10:46, Jens Marton wrote: > Dear everyone, > > I'm Jens, a computer science student from Heidelberg, Germany. I've > been wondering if "Ernie" from the example dataset exists somewhere in > a higher resolution, or - if not - if anyone knows of a (free to use) > head model with a higher reslution than Ernie. > > Kind regards > Jens Marton > > _______________________________________________ > 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 Fri Jul 1 18:13:21 2022 From: axelt at drcmr.dk (Axel Thielscher) Date: Fri, 1 Jul 2022 18:13:21 +0200 Subject: [Simnibs-discuss] Diffusion tensor information ignored In-Reply-To: <1947686326.2098614.1656501273258@mail.yahoo.com> References: <1947686326.2098614.1656501273258.ref@mail.yahoo.com> <1947686326.2098614.1656501273258@mail.yahoo.com> Message-ID: <1a7fb47c-1565-63ea-af8b-1255711343f8@drcmr.dk> Hi, giving the file name of the tensors is not enough. You also have to specify the *anisotropy_type* for each simulation list, see e.g. here*:** * https://simnibs.github.io/simnibs/build/html/documentation/sim_struct/tdcslist.html Best, Axel On 29-06-2022 13:14, Maximilian L?ckel wrote: > > 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 > > > > _______________________________________________ > 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 oulap at drcmr.dk Mon Jul 25 09:48:57 2022 From: oulap at drcmr.dk (Oula) Date: Mon, 25 Jul 2022 09:48:57 +0200 Subject: [Simnibs-discuss] Measurement of tissue volume in region of interest In-Reply-To: References: Message-ID: <7ac86513-0c58-19bd-2e59-04f59c959202@drcmr.dk> Hi Utkarsh, If you need volumes of specific neuroanatomical structures it's probably best to do a FreeSurfer run on the same scan and get those from the FS output. Best, Oula On 7/1/22 12:19, Utkarsh Pancholi wrote: > Dear sir, > > I wanted to know how I can measure a volume?of a specific region in a > brain using SimNIBS pipeline. For?example, I want to know the total > volume of the entorhinal cortex or left hippocampus. So I can relate > to the?volume?and electric field strength relationship in multiple > subjects. > > It would be a great help if you can guide in this regard. > ----------------------------------------------------------------------------------------------------- > UTKARSH V. PANCHOLI > ASSISTANT PROFESSOR > BIOMEDICAL ENGINEERING > L.D COLLEGE OF ENGINEERING > AHMEDABAD-380015 > > _______________________________________________ > 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 jesperdn at drcmr.dk Fri Jul 29 10:09:31 2022 From: jesperdn at drcmr.dk (Jesper Duemose Nielsen) Date: Fri, 29 Jul 2022 10:09:31 +0200 Subject: [Simnibs-discuss] Using Captrak coordinates for the optimization In-Reply-To: References: Message-ID: <91343cf6-0bd8-32b4-44eb-7730452e2ab3@drcmr.dk> Hi Hyoungkyu Kim Let me first apologize for the late reply! I assume you (perhaps as part of the Captrak system?) have a way of coregistering between captrak coordinates and MRI coordinates (e.g., based on fiducials)? If so, and you want the coordinates in MNI space, then you could use the function `subject2mni_coords` once you have created a headmodel using headreco (simnibs 3) or charm (simnibs 4 beta). By default, `subject2mni_coords` will apply the nonlinear deformation obtained during the segmentation. Does this do what you want? Best, Jesper On 7/1/2022 6:39, ???[ ?? / ?????? ] wrote: > > To whom it may concern, > > Hello, I am Hyoungkyu Kim, a research professor in the brain > engineering department at Korea University. First of all, I really > appreciate using your great program, SimNIBS, for my research. The > completion of the program is amazing and the tutorials are easy to > understand. > > Our team is planning to measure EEG and fMRI during the memory task > (sternberg test) under the tES stimulation, and I think SimNIBS is a > perfect solution to optimize the stimulation by using a personal T1 > image. I checked I can use personalized coordinates in the calculation > of the leadfield, and I have the coordinates of Captrak > (https://brainvision.com/products/captrak/). *I wonder if I can have > the codes or information transforming Captrak coordinates to MNI > coordinates (or to other coordinates) because I have not much > experience with the registration between two different coordinates > properly. * > * > * > It will be really helpful to me if I can have any advice from you. > Thank you so much and have a great day! > > Best, > Hyoungkyu Kim > * > * > > _______________________________________________ > 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 kim.hyoungkyu at gmail.com Fri Jul 29 10:42:51 2022 From: kim.hyoungkyu at gmail.com (Hyoungkyu Kim) Date: Fri, 29 Jul 2022 17:42:51 +0900 Subject: [Simnibs-discuss] Using Captrak coordinates for the optimization In-Reply-To: <91343cf6-0bd8-32b4-44eb-7730452e2ab3@drcmr.dk> References: <91343cf6-0bd8-32b4-44eb-7730452e2ab3@drcmr.dk> Message-ID: Hi Jesper, Thank you so much for your reply. The positions of EEG channels are scanned by the Captrak device after wearing EEG cap and we can know the actual coordinates of EEG channels. The anatomical references of the Captrak system are Nz, Cz, LPA, and RPA. I thought I need to consider and fit the reference points properly when I transfer the Captrak coordinates to the MNI Coordinate to use in SimNIBS against than simple transforming of coordinates. I wonder if my concern makes sense to you? Thank you! Best, Kyu 2022? 7? 29? (?) ?? 5:09, Jesper Duemose Nielsen ?? ??: > Hi Hyoungkyu Kim > > Let me first apologize for the late reply! > > I assume you (perhaps as part of the Captrak system?) have a way of > coregistering between captrak coordinates and MRI coordinates (e.g., based > on fiducials)? If so, and you want the coordinates in MNI space, then you > could use the function `subject2mni_coords` once you have created a > headmodel using headreco (simnibs 3) or charm (simnibs 4 beta). By default, > `subject2mni_coords` will apply the nonlinear deformation obtained during > the segmentation. Does this do what you want? > > Best, > > Jesper > On 7/1/2022 6:39, ???[ ?? / ?????? ] wrote: > > > To whom it may concern, > > Hello, I am Hyoungkyu Kim, a research professor in the brain engineering > department at Korea University. First of all, I really appreciate using > your great program, SimNIBS, for my research. The completion of the program > is amazing and the tutorials are easy to understand. > > Our team is planning to measure EEG and fMRI during the memory task > (sternberg test) under the tES stimulation, and I think SimNIBS is a > perfect solution to optimize the stimulation by using a personal T1 image. > I checked I can use personalized coordinates in the calculation of the > leadfield, and I have the coordinates of Captrak ( > https://brainvision.com/products/captrak/). *I wonder if I can have the > codes or information transforming Captrak coordinates to MNI coordinates > (or to other coordinates) because I have not much experience with the > registration between two different coordinates properly. * > > It will be really helpful to me if I can have any advice from you. > Thank you so much and have a great day! > > Best, > Hyoungkyu Kim > > > > > > _______________________________________________ > Simnibs-discuss mailing listSimnibs-discuss at drcmr.dkhttps://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss > > -------------- next part -------------- An HTML attachment was scrubbed... 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