Hi Briana,

It may be an obvious question, but did you try to compute exactly the same command but using "-t thickness" and see if the values given under "cortical thickness" differ from the one you see when running "-t pial_lgi"? Because the written label will still remain "average cortical thickness" even though the numerical values will correspond either to lgi or to thickness (see the attached screenshot).

Let me know if that was the case,

Marie

On Apr 20, 2011, at 9:12 PM, Robustelli, Briana (NIH/NIMH) [F] wrote:

Freesurfer team, I have run a group of subjects through the recon-all pipeline with the lgi option. I then looked at differences between two groups in qdec and ran a cluster correction. I would now like to extract the lgi statistics for 3 of these clusters. I have label files for these areas and tried using mris_anatomical_stats to calculate the lgi values. The script runs fine but does not appear to replace the cortical thickness values with lgi values. Below is the script I used to test it on subject "subj". Am I doing something incorrectly? Thank you.

mris_anatomical_stats -l LGI_lh_001.label -t pial_lgi -f subj/stats/lh.aparc_lgi_cluster1.stats subj lh

Briana

-- Briana Robustelli Post-Baccalaureate IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C103 10 Center Dr MSC 1366 Bethesda, MD 20892 Phone: (301) 435-4491 Briana.Robustelli@nih.gov

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