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Hello Freesurfer developers,
I am trying to map a 4D volumetric EPI image between different surfaces and I'd like a little bit of guidance as I am slightly confused about some of the outputs of freesurfer.
I have a preprocessed nifti EPI image in subject's anatomical space. First, I'd like to map this timeseries image to subject's native surface. Here is how I am currently doing this operation:
1 - Create a register.dat by using fsl identity matrix since I am already in the native space: tkregister2_cmdl --mov <epi> --fsl <ident.mat> --targ <rawavg.nii> --noedit --reg <register.dat> 2 - Then, using this register.dat to make surfaces from the 4D timeseries with: mri_vol2surf --mov <epi> --ref <anat> --reg <register.dat> --hemi lh --o <output_surface.mgz> I used these functions in the past to map statistical images to surface, but it might not be the right thing to do for timeseries in which case please let me know. Assuming this is correct though, next I want to move this native surface timeseries to fsaverage surface. I am pretty sure the calculations are in there, but I am not really sure which ones I need to use and with which freesurfer commands I can do this.
Lastly, I came across this freesurfer page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat which talks about fsaverage to native surface conversion and the examples there made me a bit confused. Aren't the surface files in the surf directory (e.g lh.pial, lh.inflated) already in the native space ? Do I need to create a lh.pial.native using these commands to overlay my timeseries image ?
Best, Ozzy