I am hoping to extract cortical thickness and volume data from FreeSurfer-processed subjects using the HCP-MMP1 atlas (Glasser et al 2016 Nature). I have found many discussions in the email list but I wasn’t able to understand whether this procedure can be reliably done using .annot files.

I have found ?h.HCPMMP1.annot files online (e.g., ggsegGlasser: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/ggseg/ggsegGlasser/tree/master/data-raw) in fsaverage space, which I have resampled to the subject’s space using mri_surf2surf as follows:

# Apply Glasser’s 2016 HCP-MMIP1.0 atlas

mri_surf2surf \

--hemi ${hemi} \

--srcsubject fsaverage \

--trgsubject ${id} \

--sval-annot fsaverage/label/${hemi}.HCPMMP1.annot \

--tval ${SUBJECTS_DIR}/${id}/label/${hemi}.HCPMMP1.annot

Then I extracted the stats using this command:

# Extract Thickness and Volume stats

mris_anatomical_stats \

-a ${SUBJECTS_DIR}/${id}/label/${hemi}.HCPMMP1.annot \

-f ${SUBJECTS_DIR}/${id}/stats/${hemi}.HCPMMP1.stats \

-b ${id} ${hemi}

My question is whether the output from this procedure can be reliably used as an accurate version of the HCP-MMP1 parcellated regions in the subject’s native space OR whether a more involved process is needed to generate the parcellation.

Thank you for your help

Best regards,

Nárlon Cássio

Nárlon C Boa Sorte Silva PhD (He, Him, His)
CIHR and MSHR BC/CLEAR Postdoctoral Research Fellow
Aging, Mobility, and Cognitive Health Lab
Djavad Mowafaghian Centre for Brain Health
Department of Physical Therapy, Faculty of Medicine
University of British Columbia
Vancouver, Canada
Twitter: @BoaNarlon