But you said your atlas is in fsaverage space, no? That is a surface-defined
space and you should map it to your subject using surf2surf, then use surf2vol
to put it in each subject's volume space
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Ren, Xueying
Sent: Tuesday, April 13, 2021 2:53 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] question about mapping fsaverage surface atlas to
subject's native volume space
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Hi Bruce,
Thanks for the reply! I didn't convert surf2surf, but convert surf2vol since my
data analysis is in volume space, do you think that might be the reason? If so,
do you have any suggestions? Thank you!
Caroline
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Fischl, Bruce
<bfis...@mgh.harvard.edu<mailto:bfis...@mgh.harvard.edu>>
Sent: Monday, April 12, 2021 10:17 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] question about mapping fsaverage surface atlas to
subject's native volume space
Did you use mri_surf2surf to map the data from fsaverage to a surface in the
subject space first?
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of Ren, Xueying
Sent: Monday, April 12, 2021 9:21 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] question about mapping fsaverage surface atlas to
subject's native volume space
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Dear experts,
I am trying to convert an atlas which is in fsaverage surface space to each
subject's native volume space. However, the alignment seems off (e.g., in the
parietal lobe, see attached screenshot). I am not sure where the problem is.
Here is the code that I used:
tkregister2 --mov ${subj_dir}/${subj_id}/mri/rawavg.mgz --targ
${subj_dir}/${subj_id}/mri/orig.mgz --reg register.native.dat --noedit
--regheader
mri_surf2vol --surfval lh.Wang2015.mgz --hemi lh --subject fsaverage
--fillribbon --reg register.native.dat --template
${subj_dir}/${subj_id}/mri/001.mgz --o lh.Wang2015.native.nii.gz
Any help would be highly appreciated! Thank you!
Caroline
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