On 5/11/2020 5:53 PM, özenç taskin wrote:
External Email - Use Caution
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>
This is ok, but unnecessary. You can use --regheader subject in
mri_vol2surf below instead of --reg
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>
Add --projfrac 0.5 to sample in the middle of the ribbon.
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.
Time series are no different than a single frame. You can actually map
directly to fsaverage in mri_vol2surf with --trgsubject fsaverage (or
you can take the vol2surf output and run mri_surf2surf on it)
Lastly, I came across this freesurfer page
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
<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 ?
No, you do not. That page just talks about if you want an actual surface
file with xyz in the native coordinates. You do not need to have this file.
Best,
Ozzy
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
