Hi Luke,

Can you try to pass the full path to your label file?  Instead of ‘rh.c1.label’, pass ‘/Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label’ to mri_segstats.

I think that should work.

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Luke K Harper
Sent: Friday, December 2, 2022 5:14 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] LGI label statistics

        External Email - Use Caution        

Dear freesurfer,

I am attempting to extract LGI statistical data from a label running the mri_segstats command

Here is the script I am attempting to run:

mri_segstats --slabel A152 rh rh.c1.label --i $SUBJECTS_DIR/A152/surf/rh.pial_lgi --sum rh.aparc.pial_lgi.stats

This returns an error: error: mri_segstats: could not open label file rh.c1.label

I created the label using freeview - make closed path - then filling the closed path. The label projects on pial and inflated surfaces

Furthermore the label is able to be identified and used in the following command

mris_anatomical_stats \

-l /Users/lu8342ha/Desktop/subjects/A152/label/rh.c1.label \

-f /Users/lu8342ha/Desktop/subjects/A152/stats/rh.c1.stats \

A152 \

rh

Please could you advise me on where I am going wrong here?

Many thanks,

Luke