Dear Freesurfer experts,
Happy new year!
I encountered an issue with the quantifyHAsubregions.sh command as I tried to extract amygdala subnuclei values from a previously segmented dataset. I tried both commands below, specifying the version (v20) and not: quantifyHAsubregions.sh amygNuc T1 All_Amyg [subjects_dir] quantifyHAsubregions.sh amygNuc T1.v20 All_Amyg [subjects_dir]
The command did not run. No error message was given. It just skipped to a new command line. Please see attached for a screenshot.
The recon was done in Freesurfer 5.3 and the sample size is very big (~1400). I wonder if that or anything else could be causing the problem. Any guidance is immensely appreciated!
Thank you! Wisteria
Wisteria Deng Clinical Research Coordinator Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Rm 2611 Charlestown, MA 02129 Phone: 617-643-4441
