Dear FreeSurfer experts,
I am currently in the process of running the mris_anatomical_stats command line to look at cortical thickness however, the output states that the annotation file could not be read.
Please see below for command line and output:
navenalingum% mris_anatomical_stats -a N1/label/lh.aparc.annot -b N1 lh
computing statistics for each annotation in N1/label/lh.aparc.annot.
reading volume /Users/navenalingum/Applications/freesurfer/subjects/N1/mri/wm.mgz...
reading input surface /Users/navenalingum/Applications/freesurfer/subjects/N1/surf/lh.white...
reading input pial surface /Users/navenalingum/Applications/freesurfer/subjects/N1/surf/lh.pial...
reading input white surface /Users/navenalingum/Applications/freesurfer/subjects/N1/surf/lh.white...
could not read annot file N1/label/lh.aparc.annot
No such file or directory
mris_anatomical_stats: could not read annotation file N1/label/lh.aparc.annot
No such file or directory
Could it be that there was an error in the recon-all processing stage?
Your help would be greatly appreciated!
Thanks,
Navena Lingum