On 10/13/2020 5:42 AM, Maron M. wrote: > External Email - Use Caution > > 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...) 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.
> 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?) 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 > > 3) > 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! > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
