On 10/13/2020 5:42 AM, Maron M. wrote:
External Email - Use CautionDear Freesurfer Team,
I need to move an atlas file, Shen268 in 2mm (https://www.nitrc.org/frs/download.php/7977/shen_2mm_268_parcellation.nii.gz) from volumetric into surface space in order to do some analysis in MATLAB with it. Specifically, I need the atlas file as .annot and a .sphere (I think this would be from the anatomical template).
So far, I have not succeeded. I believe it is some combination of recon-all, mri_vol2surf and mris_seg2annot, however the details are unclear.
I think the initial problem is with the recon all. In this question (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg63687.html) it says I should recon-all the "anatomical template". Could you elaborate which template that is? Its not the atlas file itself, but just some T1 in the same space?
And that will give me the file necessary for the --reg command in mri_vol2surf, I guess?
Sofar, I think this is what I have to do:
Recon-all -all -i "anatomical_template" (I am stuck here already, since I don't know what to recon-all here...)
Yes, the template is an anatomical T1-weighted image in the same space as your atlas. Usually, this would be a volume that you would register your individual subjects to to get them into the atlas space (eg, the MNI152 volume). Run recon-all on that.
mri_vol2surf --src atlas_file.nii --out outputfile_rh.mgz --hemi rh --projfrac 0.5 (--trgsubject fsaverage or —reg register.dat from recon-all?)
Use --regheader subject where subject is the name of the subject you gave during recon-all. If you need to have the output in fsaverage space, you can add --trgsubject fsaverage
mris_seg2annot --seg outputfile_rh.mgz --s fsaverage --h rh --ctab-auto --o atlas_rh.annot
This should work (but use subject instead of fsaverage if subject used in mri_vol2surf). Also, you'll probably want to call the output rh.atlas.annot
I would be very thankful for any suggestions and support. Best and thanks a lot!
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