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Awesome, thanks Doug. That's pretty helpful. I should also use the orig.mgz
with tkregister2 instead of rawavg.mgz if the aim is to get surface maps in
native space, am I right ? And by native space I mean the subjects' native
brain structure and not necessarily the native xyz coordinates (I guess
conformed space is the right term for this, but I am not sure).
Best,
Ozzy
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
Sent: Wednesday, May 13, 2020 3:07 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Volume timeseries to native and fsaverage
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 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
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