From w.tomasz at sensusmed.pl Tue Aug 18 17:37:11 2020 From: w.tomasz at sensusmed.pl (w.tomasz at sensusmed.pl) Date: Tue, 18 Aug 2020 17:37:11 +0200 Subject: [Simnibs-discuss] manual correction Message-ID: Hello, I had the pleasure of talking to you for a while at the April webinar on brain modeling after stroke. I am currently researching the use of stimulation in a person with tinnitus with personalized stimulation. I have a question about the manual correction of the brain model (the model created from the t1_mprage_sag and t2_space_dark_fluid_sag_p2 images) in the automatic model creation in the CAT report gets results on the B and B + levels. I'm a beginner when it comes to modeling (I am more concerned with NIBS in clinical applications), sorry if my questions are trivial : 1. on the SIMNIBS website, it says that it is not possible to do CAT cuttings, whether in such a system we use "m2m_ernie \ mask_prep \ MASK_CAT_WM.nii.gz" or "m2m_ernie \ gm.nii.gz" for manual editing. Does a manual correction make sense in such a situation? 2. From your and your team's experience, how big are the differences in electric field distributions between the B / B + and A-level models? 3.I wanted to use ITK-SNAP for the correction proposed on one of your toutorials but I am a beginner I have a hard time figuring out how to check if (how exactly) the surface contours follow the tissue shapes in the T1w image, with more masks than one . 4. Could you suggest a program other than FS to evaluate the created model? Since I'm a Windows 10 and FS user, it's more complicated here. Thank you very much for your help and your time! Best regards, -- Witold Tomasz psycholog, psychoterapeuta, terapeuta tDCS O?rodek psychoterapii i neurorehabilitacji Sensusmed Witold Tomasz p: 504288040 m: 789335047 a: Krak?w 30-303 ul.Madali?skiego 3/1 w: www.sensusmed.pl [1] e: w.tomasz at sensusmed.pl Links: ------ [1] http://www.sensusmed.pl -------------- next part -------------- An HTML attachment was scrubbed... URL: From oupu at dtu.dk Wed Aug 19 13:36:32 2020 From: oupu at dtu.dk (Oula Puonti) Date: Wed, 19 Aug 2020 11:36:32 +0000 Subject: [Simnibs-discuss] manual correction In-Reply-To: References: Message-ID: <2392cc26e2e34ee5a6c4e8f63bea1f94@dtu.dk> Hi Witold, 1) When using CAT the cortical and white matter surfaces are not generated from the volume files (.nii.gz), but rather the surface files stored in the mask_prerp folder. Thus editing the volume files will have no effect on the cortical or white matter surfaces in the final headmodel. You can, however, edit the CSF, skull, and scalp masks and these edits are propagated to the final head model. If you want to edit the GM and WM masks, please disable CAT12 (--no-cat flag). After that the edits on the WM and GM masks will also change the final headmodel. 2) We have not studied this systematically, but in my experience CAT12 does a good job even if the grade it assigns is B. That being said, you should still inspect the resulting segmentation for large errors using the headreco check call. 3 & 4) I'm not that experienced with manual edits and the little experience I have is limited to freeview. I've heard people succesfully using ITK snap, but if you find it too difficult, I would consider using freeview through the windows subsystem for linux. It's a bit trickier, but the instructions here are quite clear: https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport Best, Oula ________________________________ From: Simnibs-discuss on behalf of w.tomasz at sensusmed.pl Sent: Tuesday, August 18, 2020 5:37:11 PM To: Guilherme B Saturnino Cc: discuss at simnibs.org Subject: [Simnibs-discuss] manual correction Hello, I had the pleasure of talking to you for a while at the April webinar on brain modeling after stroke. I am currently researching the use of stimulation in a person with tinnitus with personalized stimulation. I have a question about the manual correction of the brain model (the model created from the t1_mprage_sag and t2_space_dark_fluid_sag_p2 images) in the automatic model creation in the CAT report gets results on the B and B + levels. I'm a beginner when it comes to modeling (I am more concerned with NIBS in clinical applications), sorry if my questions are trivial : 1. on the SIMNIBS website, it says that it is not possible to do CAT cuttings, whether in such a system we use "m2m_ernie \ mask_prep \ MASK_CAT_WM.nii.gz" or "m2m_ernie \ gm.nii.gz" for manual editing. Does a manual correction make sense in such a situation? 2. From your and your team's experience, how big are the differences in electric field distributions between the B / B + and A-level models? 3.I wanted to use ITK-SNAP for the correction proposed on one of your toutorials but I am a beginner I have a hard time figuring out how to check if (how exactly) the surface contours follow the tissue shapes in the T1w image, with more masks than one . 4. Could you suggest a program other than FS to evaluate the created model? Since I'm a Windows 10 and FS user, it's more complicated here. Thank you very much for your help and your time! Best regards, -- [https://drive.google.com/uc?id=0B_hgtJUYICqhM3dUUE1PSlpjQTQ] Witold Tomasz psycholog, psychoterapeuta, terapeuta tDCS O?rodek psychoterapii i neurorehabilitacji Sensusmed Witold Tomasz p: 504288040 m: 789335047 a: Krak?w 30-303 ul.Madali?skiego 3/1 w: www.sensusmed.pl e: w.tomasz at sensusmed.pl -------------- next part -------------- An HTML attachment was scrubbed... URL: From nkaur at wakehealth.edu Wed Aug 19 17:27:41 2020 From: nkaur at wakehealth.edu (Navneet Kaur) Date: Wed, 19 Aug 2020 15:27:41 +0000 Subject: [Simnibs-discuss] Updated SIMNIBS Version Message-ID: Hi, I am in the process of downloading SIMNIBS. I recently read that there is going to be an updated version of SIMNIBS available. Checking in to see if the updated SIMNIBS will be available soon or if I should move forward with the current SIMNIBS version. Best, Nav ---------------------------------------------------------- Navneet Kaur, Ph.D. Research Fellow Clinical Neuromodulation Laboratory Department of Cancer Biology Wake Forest University School of Medicine nkaur at wakehealth.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Thu Aug 20 09:06:46 2020 From: guilhermebs at drcmr.dk (Guilherme Saturnino) Date: Thu, 20 Aug 2020 09:06:46 +0200 Subject: [Simnibs-discuss] Updated SIMNIBS Version In-Reply-To: References: Message-ID: Hello, We will likely release version 3.2, which features new TMS and TES optimization options, very soon (probably on 21/08). After that, the next feature release, with a new head modelling pipeline, will take a few months. Best Regards, Guilherme On 8/19/20 5:27 PM, Navneet Kaur wrote: > > Hi, > > I am in the process of downloading SIMNIBS. I recently read that there > is going to be an updated version of SIMNIBS available. Checking in to > see if the updated SIMNIBS will be available soon or if I should move > forward with the current SIMNIBS version. > > Best, > > Nav > > ---------------------------------------------------------- > > Navneet Kaur, Ph.D. > > Research Fellow > > Clinical Neuromodulation Laboratory > > Department of Cancer Biology > > Wake Forest University School of Medicine > > nkaur at wakehealth.edu > > > _______________________________________________ > 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 pdhami06 at gmail.com Tue Aug 25 13:34:48 2020 From: pdhami06 at gmail.com (Paul Dhami) Date: Tue, 25 Aug 2020 07:34:48 -0400 Subject: [Simnibs-discuss] E-field modelling using MNI coordinates of where TMS was applied Message-ID: Dear SIMNIBS community, I am new to SIMNIBS, so apologizes in advance for what may be an easy question. In a TMS-EEG study, TMS was used on 4 cortical sites independently. The sites were targeted across all participants using the same MNI coordinates (acquired from the literature). However, I do not have the precise world coordinates of the coil. I only have the MNI coordinates that were targeted. Because I do not have the world coordinates of where the TMS coil was located for each participant (nor the nearest targeted electrode), is E-field modelling with SIMNIBS still possible? Any insight would be greatly appreciated. Best wishes, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From oupu at dtu.dk Fri Aug 28 15:25:31 2020 From: oupu at dtu.dk (Oula Puonti) Date: Fri, 28 Aug 2020 13:25:31 +0000 Subject: [Simnibs-discuss] E-field modelling using MNI coordinates of where TMS was applied In-Reply-To: References: Message-ID: <348e4f1b3e9d48a8b156ab3ef08d8c39@dtu.dk> Hi Paul, We have a command line tool called mni2subject_coords, which converts mni coordinates into the subject space. https://simnibs.github.io/simnibs/build/html/documentation/command_line/mni2subject_coords.html If you type mni2subject_coords -h you'll get information on how to use the tool to convert specific coordinates instead of using .csv files. You can then transform the coil positions that are in MNI space to the subject space, set the coil direction for each subject individually, and run the simulation. In case you also have the direction in MNI space this can also be transformed to the subject space using the mni2subject_coords tool, but in this case you need to create a .csv file with a specific CoilPos tag (see the help). Let us know if you need help with this. Best, Oula ________________________________ From: Simnibs-discuss on behalf of Paul Dhami Sent: Tuesday, August 25, 2020 1:34:48 PM To: discuss at simnibs.org Subject: [Simnibs-discuss] E-field modelling using MNI coordinates of where TMS was applied Dear SIMNIBS community, I am new to SIMNIBS, so apologizes in advance for what may be an easy question. In a TMS-EEG study, TMS was used on 4 cortical sites independently. The sites were targeted across all participants using the same MNI coordinates (acquired from the literature). However, I do not have the precise world coordinates of the coil. I only have the MNI coordinates that were targeted. Because I do not have the world coordinates of where the TMS coil was located for each participant (nor the nearest targeted electrode), is E-field modelling with SIMNIBS still possible? Any insight would be greatly appreciated. Best wishes, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From w.tomasz at sensusmed.pl Fri Aug 28 22:20:54 2020 From: w.tomasz at sensusmed.pl (w.tomasz at sensusmed.pl) Date: Fri, 28 Aug 2020 22:20:54 +0200 Subject: [Simnibs-discuss] manual correction In-Reply-To: <2392cc26e2e34ee5a6c4e8f63bea1f94@dtu.dk> References: <2392cc26e2e34ee5a6c4e8f63bea1f94@dtu.dk> Message-ID: Hi Oula, Thanks for your answers and suggestions. 1)If I understand correctly, the final headform in the B and B + ranges will be sufficient to calculate the optimal stimulation if I first check with Freesurfer for large deviations in bone and skin mapping ? 2)Is it possible to use software to calculate appropriate electrode placement for transcranial temporal interference stimulation? Of course also to visualize the distribution of the electric field. For example, for fields with a frequency of 200 and 210 Hz. The area of interest is the L-amygdala. Best regards, Witold W dniu 2020-08-19 13:36, Oula Puonti napisa?(a): > Hi Witold, > > 1) When using CAT the cortical and white matter surfaces are not > generated from the volume files (.nii.gz), but rather the surface > files stored in the mask_prerp folder. Thus editing the volume files > > will have no effect on the cortical or white matter surfaces in the > final headmodel. You can, however, edit the CSF, skull, and scalp > masks and these edits are propagated to the final head model. > > If you want to edit the GM and WM masks, please disable CAT12 > (--no-cat flag). After that the edits on the WM and GM masks will also > change the final headmodel. > > 2) We have not studied this systematically, but in my experience CAT12 > does a good job even if the grade it assigns is B. That being said, > you should still inspect the resulting segmentation for large errors > using the > > headreco check call. > > 3 & 4) I'm not that experienced with manual edits and the little > experience I have is limited to freeview. I've heard people > succesfully using ITK snap, but if you find it too difficult, I would > consider using freeview through the windows subsystem for linux. It's > a bit trickier, but the instructions here are quite clear: > > https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport > > Best, > Oula > ------------------------- > > From: Simnibs-discuss on behalf of > w.tomasz at sensusmed.pl > Sent: Tuesday, August 18, 2020 5:37:11 PM > To: Guilherme B Saturnino > Cc: discuss at simnibs.org > Subject: [Simnibs-discuss] manual correction > > Hello, > > I had the pleasure of talking to you for a while at the April webinar > on brain modeling after stroke. > I am currently researching the use of stimulation in a person with > tinnitus with personalized stimulation. > I have a question about the manual correction of the brain model (the > model created from the t1_mprage_sag and t2_space_dark_fluid_sag_p2 > images) in the automatic model creation in the CAT report gets results > on the B and B + levels. > I'm a beginner when it comes to modeling (I am more concerned with > NIBS in clinical applications), sorry if my questions are trivial : > > 1. on the SIMNIBS website, it says that it is not possible to do CAT > cuttings, whether in such a system we use "m2m_ernie \ mask_prep \ > MASK_CAT_WM.nii.gz" or "m2m_ernie \ gm.nii.gz" for manual editing. > Does a manual correction make sense in such a situation? > > 2. From your and your team's experience, how big are the differences > in electric field distributions between the B / B + and A-level > models? > > 3.I wanted to use ITK-SNAP for the correction proposed on one of your > toutorials but I am a beginner I have a hard time figuring out how to > check if (how exactly) the surface contours follow the tissue shapes > in the T1w image, with more masks than one . > > 4. Could you suggest a program other than FS to evaluate the created > model? Since I'm a Windows 10 and FS user, it's more complicated here. > > Thank you very much for your help and your time! > Best regards, > -- > > Witold Tomasz > > psycholog, psychoterapeuta, terapeuta tDCS > > O?rodek psychoterapii i neurorehabilitacji > > Sensusmed Witold Tomasz > > p: > 504288040 m: 789335047 > > a: > Krak?w 30-303 > > ul.Madali?skiego 3/1 > > w: > www.sensusmed.pl [1] [1 [1]] e: w.tomasz at sensusmed.pl > > Links: > ------ > [1] http://www.sensusmed.pl -- Witold Tomasz psycholog, psychoterapeuta, terapeuta tDCS O?rodek psychoterapii i neurorehabilitacji Sensusmed Witold Tomasz p: 504288040 m: 789335047 a: Krak?w 30-303 ul.Madali?skiego 3/1 w: www.sensusmed.pl [1] e: w.tomasz at sensusmed.pl Links: ------ [1] http://www.sensusmed.pl -------------- next part -------------- An HTML attachment was scrubbed... URL: