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Hi all,

I'm trying to use the Glaser atlas (HCP-MMP1) to get thickness, volume, and area measures for an existing fs-subject, meaning that the standard recon-all was already performed. I was able to extract some measures, but it would be nice to get verified that my approach is valid. I'm using FreeSurfer 7.1 and have already applied standard recon-all to all my subjects.

The following variables are used: $subjid = folder name of the recon-all output for a specific subject $hcpdir = the directory where I stored the annotation files for the hcp-atlas

I got annotation files with the atlas projected onto fsaverage from here https://secure-web.cisco.com/1I7iKyRV6ybWIIhCzcBweKSPq9s7w7SmrhQN_FfL8XYj8j0....

Then I applied the annotation files to get the statistics file using: mris_anatomical_stats -th3 -mgz -cortex $subjid/label/lh.cortex.label -f lh.hcp.stats -b -a $hcpdir/lh.HCP-MMP1.annot f475 lh white

Subsequently, I used the following commands to extract measures in CSV files. aparcstats2table --delimiter comma --subjects $subjid --parc hcp --hemi lh --meas area --transpose --tablefile lh_hpc_area_stats.csv aparcstats2table --delimiter comma --subjects $subjid --parc hcp --hemi lh --meas volume --transpose --tablefile lh_hpc_volume_stats.csv aparcstats2table --delimiter comma --subjects $subjid --parc hcp --hemi lh --meas thickness --transpose --tablefile lh_hpc_thickness_stats.csv

Is this a valid approach, and would I get meaningful values, or would I have to run some other additional steps?

Kind regards, Ruben Dörfel.