1) mri_surf2surf --srcsubject fsaverage --trgsubject $SubjectID --hemi lh --sval-annot /ourSchaferAtlasDirectory/label/lh.Schaefer2018_400Parcels_7Networks_order.annot --tval ourSubjectDirectory/label/lh.Schaefer2018_400Parcels_7Networks_order_native.annot
2) the same of 1) for the right hemisphere
3) mri_label2vol --annot ourSubjectDirectory/label/lh.Schaefer2018_400Parcels_7Networks_order_native.annot --temp ourSubjectDirectory/mri/our T1.nii --o ourSubjectDirectory/mri/sch_lh.mgz --subject $SubjectID --identity --hemi lh
4) the same of 3) for the right hemisphere
5) mri_concat ourSubjectDirectory/mri/sch_lh.mgz ourSubjectDirectory/mri/sch_rh.mgz --sum --o ourSubjectDirectory/mri/sch_lh+rh.mgz
However, at this point, the resulting .mgz file (sch_lh+rh.mgz) is a bit strange : When I open the file in matlab, I see that it's volume field is 218*182*182 , while the same data results in 256*256*256 for Destrieux Atlas. Furthermore, values of the volume field of sch_lh+rh.mgz change between 0-200 , while this is 0-12175 for the Destrieux Atlas. These effects are also apparent in the ultimate results (parcellation.nii images, which I generate by using .mgz files). They are not aligned properly and their intensity is also erroneous. I suspect that we have a mistake in the above pipeline.
My questions are:
1) Is there simpler way to do this task? (For example, a simple addition to the recon-all function, etc.)
2) If not, what else should I do to be able to get the correct parcellations ?
PS: I am a bit new to the FreeSurfer and MRI processing, so please accept my apologizes if this is a simple question...
Thank you in advance and best regards.