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Dear 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:
1) Recon-all -all -i "anatomical_template" (I am stuck here already, since I don't know what to recon-all here...)
2) mri_vol2surf --src atlas_file.nii --out outputfile_rh.mgz --hemi rh --projfrac 0.5 (--trgsubject fsaverage or —reg register.dat from recon-all?)
3) mris_seg2annot --seg outputfile_rh.mgz --s fsaverage --h rh --ctab-auto --o atlas_rh.annot
I would be very thankful for any suggestions and support. Best and thanks a lot!