From ikko9371787 at gmail.com Tue Jun 2 11:09:19 2020 From: ikko9371787 at gmail.com (=?UTF-8?B?5pyo5p2R5LiA55qT?=) Date: Tue, 2 Jun 2020 18:09:19 +0900 Subject: [Simnibs-discuss] mri2mesh or headreco for macaque? Message-ID: Dear all, I'm trying to use simnibs for macaque T1w and T2w MRI data. Does anybody guide me the best way to create head models from these data? Anyway, I managed to get 5 segmented labels as with mri2mesh with following steps. Are there any ways to use these nifti mask to create head models? 1. Get WM, GM, cerebellum, following HCP-NHP pipelines(nearly the same with freesurfer). https://github.com/Washington-University/NHPPipelines 2. Get scalp and skull from mri_watershed 3. Get CSF from FAST in FSL Thanks in advance, Ikko -------------- next part -------------- An HTML attachment was scrubbed... URL: From giacomo.bertazzoli at unitn.it Thu Jun 11 19:39:57 2020 From: giacomo.bertazzoli at unitn.it (Giacomo Bertazzoli) Date: Thu, 11 Jun 2020 19:39:57 +0200 Subject: [Simnibs-discuss] Scalp to cortex distance Message-ID: Dear all, I am trying to extract the information about the scalp to cortex distance under the TMS coil. After I have defined the position of the coil on the scalp (by either coordinate or electrode position), is there a way to calculate the distance between that position on the scalp and its projection on the cortical surface? Thanks in advance, 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From romanellasara at gmail.com Fri Jun 12 11:51:03 2020 From: romanellasara at gmail.com (Sara Romanella) Date: Fri, 12 Jun 2020 11:51:03 +0200 Subject: [Simnibs-discuss] Doubt about Mesh Message-ID: To whom it may concern, I am Sara Romanella, a PhD Student in Florence. I am using your software for modeling in healthy subjects and I found it incredibly helpful and intuitive. I just have a couple of doubts. If there is any chance you could enlighten me, this would be greatly appreciated. I am working on MatLab script with your last version on Windows. - The mesh created by SimNiBS thanks to headreco is a volumetric mesh? Or it only creates a surface mesh? - Can I transform and save the resulting mesh as a nifti file in matlab? - Can extract the mean of the field withing an entire network while analyzing the simulation (post-hoc)? In any case, thank you so much for any information you can give me. Best, Sara Sara Romanella Fellow (Ph.D. in Neuroscience) Phone nr. +393409831115 Personal Mail: romanellasara at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Fri Jun 12 15:57:29 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Fri, 12 Jun 2020 15:57:29 +0200 Subject: [Simnibs-discuss] Doubt about Mesh In-Reply-To: References: Message-ID: <266b6e60-bebe-1b92-6e23-99f8a8ff189b@drcmr.dk> Hello, Thanks for your interest in SimNIBS! /- The mesh created by SimNiBS thanks to headreco is a volumetric mesh? Or it only?creates a surface mesh? / The final mesh (.msh) contains both a volume mesh with tetrahedral elements and a surface mesh with triangular elements. The numerical method we for the simulations (FEM) requires volume meshes. You can find surfaces in the m2m_/subID/ folder as well (.stl format). /- Can I transform and save the resulting mesh as a nifti file in matlab?/ / / We create a nifti image based on the mesh file. It is called /subID/_final_contr.nii.gz, and is located in the m2m/_subID/ folder. /- Can extract the mean of the field withing an entire network while analyzing the simulation (post-hoc)?/ / / Sure, but the exact analysis pipeline will depend on how the network is defined, e.g. FsAverage space or MNI space. SimNIBS can transform electric field simulations to both, please see the tutorial: https://simnibs.github.io/simnibs/build/html/tutorial/gui.html#setting-simulation-options Best Regards, Guilherme // On 12/06/2020 11.51, Sara Romanella wrote: > To whom it may concern, > > I am Sara Romanella, a PhD Student in Florence. I am using your > software for modeling in healthy subjects and I found it > incredibly?helpful and intuitive. I just have a couple?of doubts. If > there is any chance you could enlighten me, this?would be greatly > appreciated. I am working on MatLab script?with your last version on > Windows. > > - The mesh created by SimNiBS thanks to headreco is a volumetric mesh? > Or it only?creates a surface mesh? > - Can I transform and save the resulting mesh as a nifti file in matlab? > - Can extract the mean of the field withing an entire network while > analyzing the simulation (post-hoc)? > > In any case, thank you so much for any information you can give me. > Best, > Sara > > Sara Romanella > Fellow (Ph.D. in Neuroscience) > Phone nr. +393409831115 > Personal Mail: romanellasara at gmail.com > > > _______________________________________________ > 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 guilhermebs at drcmr.dk Fri Jun 12 16:08:43 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Fri, 12 Jun 2020 16:08:43 +0200 Subject: [Simnibs-discuss] Scalp to cortex distance In-Reply-To: References: Message-ID: Hello, I have just added this to the standard output for the next SimNIBS version. If you want to calculate this now, you will have to: 1. Determine the coil position, for example in the GUI or looking at the last row of the /matsimnibs/ matrix, in the SimNIBS output 2. Load the mesh in python or matlab 3. Calculate the distances between the gray matter surface triangles (tag 1002) and the coil in python or matlab. For steps 2-3, these functions might help: MATLAB: /mesh_load_gmsh4 /to load the mesh, /mesh_extract_regions/ to get the gray matter surface, and /mesh_get_triangle_centers /to calculate the positions of the tiangles // PYTHON: /mesh = simnibs.read_msh/ to load the mesh, /mesh.crop_mesh /to get the gray matter surface, and /mesh.elements_baricenters/()[:] to calculate the positions of the triangles. Best Regards, Guilherme On 11/06/2020 19.39, Giacomo Bertazzoli wrote: > Dear all, > > I am trying to extract the information about the scalp to cortex > distance under the TMS coil. > After I have defined the position of the?coil on the scalp (by either > coordinate or electrode position), is there a way to calculate the > distance between that position on the scalp and its projection on the > cortical surface? > > Thanks in advance, > 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 > > _______________________________________________ > 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 td5u19 at soton.ac.uk Thu Jun 25 20:17:05 2020 From: td5u19 at soton.ac.uk (du t. (td5u19)) Date: Thu, 25 Jun 2020 18:17:05 +0000 Subject: [Simnibs-discuss] simNIBS question Message-ID: Hello, I am a Msc student who is doing my graduate project based on simNIBS. I want to do the TACs simulation to know if machine learning can use to find the right parameters (AC frequency, current, electrode location etc.) to produce interference at target specific brain area. So is it possible to visualize the effect brought by AC frequency change on simNIBS? Or is there any some code examples for AC simulation that gives a complete process to scale and sum electric fields from different simulations to obtain oscillating AC electric field as you explained in FAQ? Any further replay is appreciated, thanks a lot and have a nice day. Best, Tianyu Du -------------- next part -------------- An HTML attachment was scrubbed... URL: From guilhermebs at drcmr.dk Fri Jun 26 10:48:29 2020 From: guilhermebs at drcmr.dk (Guilherme B Saturnino) Date: Fri, 26 Jun 2020 10:48:29 +0200 Subject: [Simnibs-discuss] simNIBS question In-Reply-To: References: Message-ID: <159b0d1b-32cc-32e8-9c9a-6d836f38ad57@drcmr.dk> Hello, Thanks a lot for the interest in SimNIBS! As mentioned in the FAQ, the osculations in TACS do not change the electric field spread, but act as a scaling factor as the time and spatial component are separable E(x, t) = E(x)I(t). If you have many electrodes at different phases, it becomes a little more complicated, but it is still a linear superposition (please see https://doi.org/10.1016/j.neuroimage.2017.09.024). To calculate it you can just use our matlab or python modules to load simulation results (mesh_load_gmsh4 in matlab or simnibs.read_msh in python, please see https://github.com/simnibs/simnibs/tree/master/simnibs/examples/analysis for examples). We also have a module to optimize electrode locations (https://simnibs.github.io/simnibs/build/html/tutorial/optimization.html) and a paper about it (https://doi.org/10.1016/j.neuroimage.2019.116183). Best, Guilherme On 25/06/2020 20.17, du t. (td5u19) wrote: > > Hello, > > ?? I am a Msc student who is doing my graduate project based on > simNIBS. I want to do the TACs simulation to know if machine learning > can use to find the right parameters (AC frequency, current, electrode > location etc.) to produce interference at target specific brain area. > ?So is it possible to visualize the effect brought by AC frequency > change on simNIBS? Or is there any some code examples for AC > simulation that gives a complete process to scale and sum electric > fields from different simulations to obtain oscillating AC electric > field as you explained in FAQ? > > ? ?Any further replay is appreciated, thanks a lot and have a nice day. > > Best, > > Tianyu Du > > > _______________________________________________ > 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: