Hi Navena

hmmm, sounds like that subject didn't finish processing for some reason. You could try rerunning just that step with:

recon-all -s N1 -sd /Users/navenalingum/Applications/freesurfer/subjects -cortparc -cortparc2 -cortparc3

and see if that completes (it should only take a couple of min). If not, you might have to start earlier in the process.

Bruce

On Mon, 13 Jun 2016, Navena Rebecca Lingum wrote:

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