Find volumes of each ROI in Freesurfer outputs

Good morning everyone :sparkles:
I have a question about how to find the mean thickness as well as volume of gray matter and white matter for each regions of interest after brain image processing with FreeSurfer, where can I find these values?
Also, is it possible to print it in an excel file for a group of subjects in a folder instead of showing it to each subject independently?

The values I want are the same as the values in the attached picture.
Thanks in advance


How are you defining your ROIs?


I want to compare cortical thickness values and the size of gray and white matter to different areas in Atlas Desikan-Killiany atlas. Then select the best group of them.

Did I miss something?

These values are in /$FREESURFER_DIR/$SUBJECT/stats/rh.aparc.DKTatlas.stats and /$FREESURFER_DIR/$SUBJECT/stats/lh.aparc.DKTatlas.stats.

1 Like

thank you so much :sparkles: :pray:t2:
Is there a way to print or display the values of all patients at once?

The following will print the contents of all such stats files to terminal. cat /$FREESURFER_DIR/*/stats/rh.aparc.DKTatlas.stats

1 Like