oh, if you want them in conformed space, they are already there
On 5/18/2020 11:34 AM, özenç taşkın wrote:
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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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