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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@mgh.harvard.edu Sent: Monday, April 12, 2021 10:17 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

Did you use mri_surf2surf to map the data from fsaverage to a surface in the subject space first?

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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 Subject: [Freesurfer] question about mapping fsaverage surface atlas to subject's native volume space

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External Email - Use Caution

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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Hi Bruce,

I tried your suggestion, and it worked perfectly. Thank you so much!

Best, Caroline -- (Caroline) Xueying Ren Graduate Student Department of Psychology University of Pittsburgh she/her/hers

xur1@pitt.edu

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@mgh.harvard.edu Sent: Tuesday, April 13, 2021 2:55 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

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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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

External Email - Use Caution

External Email - Use Caution

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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce <BFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu> Sent: Monday, April 12, 2021 10:17 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] question about mapping fsaverage surface atlas to subject's native volume space

External Email - Use Caution

External Email - Use Caution

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