Hi there, 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: https://secure-web.cisco.com/1RCrRYR2kfqIYN7pxC6sGgF_XvdqzAAephS3DadIADfMm-6hoRd0sxcmdWRwYcGtkA-1gc7ZC9mYwzkPFHM8ycIPc3lYKBliI4MlhpBI0pNP7d6nNXhKmziozV7LPHR6bOmLuljZCo6Elu5DfPrDjcK9sXxOTADtFMn_j7QiamMngwTj6ci-kK7weiVMNm48V-1lppYtYxYIF2o33pH_y3e0U1uQqglVKzEK9L4W50PlIBDYIetkga5KuLV3JZ3qULjZufEAQgsKcBIZ09jnE1GKxMWrAVDgQWUqbas9gFiJnELS_7FBm92O9x6kP22Zn/https%3A%2F%2Fgithub.com%2Fggseg%2FggsegGlasser%2Ftree%2Fmaster%2Fdata-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
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