Re: [Freesurfer] Overlay electric field distribution on pial surface

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Dear Prof. Fischl,

Sorry for the lack of clarity. I used bbregister to generate a registration.dat file. I used simnibs to calculate the Efield distribution and this has the option to convert the Efield mesh files to .nii files. So I registered the high resolution T1 (from simnibs, that aligns with the Efield) to the original T1 data. Consecutively, I used tksurfer to visualize.

bbregister --s Dep48_T1_origANAT --mov /home/debby/Desktop/FigModPap_Depr48/fs_HeadmeshDep48_origT1/mri/T1.mgz --reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat --t1

tksurfer FigModPap_Depr48 lh pial -sdir /home/debby/Desktop -overlay /home/debby/Desktop/FigModPap_Depr48/Dep48_DLPFC_normE_CORRECTED.nii -overlay-reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat -fthresh -2 -fmid 150

Best, Debby ________________________________________ Van: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] namens Bruce Fischl [fischl@nmr.mgh.harvard.edu] Verzonden: zaterdag 15 september 2018 17:21 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface

Hi Debby

you need to give us a lot more information. What commands did you use to sample the field onto the surface? What was the output of those commands? Note that tksurfer is deprecated, so I wouldn't worry about how it looks

cheers Bruce

On Sat, 15 Sep 2018, Meusen - Klooster, D.C.W. wrote:

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Dear all, I am studying transcranial magnetic stimulation (TMS) and would like to nicely visualize my TMS induced electric fields over a pial surface, preferably using Freesurfer to stay in line with my other images. I have a .nii file of the electric field distribution, registered to T1, representing field strengths in every voxel. Visualization in freeview looks okay, but visualization using tksurfer does not really give the right results (most of the brain is yellow... no field distribution visible). I guess something goes wrong in the setting of the colorbar. Preferably I would like to see the field strengths (min:max) in a blue-red colorscheme. Can anybody tell me how to accomplish this? Thank you very much in advance. Best, Debby