External Email - Use Caution
Dear FreeSurfer developers *For my MRI data, I have cortical parcellations and segmentations for the Destrieux and Desikan-Killiany atlases. Now, **I am attempting to use Schaefer 2018 atlas (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal) for cortical parcellation together with FreeSurfer. Currently what I have tried is:*
*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.