Hi Rashmi, Could you check that the ?h.aparc.stats for the subjects exist and contain actual measurements? If not, check the <subjid>/scripts/recon-all.log to see if the -parcstats step failed. Also, double-check your SUBJECTS_DIR path is correct. -Louis

On Wed, 25 Jan 2012, Rashmi Singh wrote:

Hello, I was trying to get the cortical thickness in the table format for all of my subjects on which I had run recon all. I see the stats folder with rh/lh.aparc.stats files. My command was: aparcstats2table --subjects AA471.T1 AA471.T2 AA471.T3 AA474.T0 AA476.T0 AA479.T0 AA483.T0 AA483.T2 AA483.T3 AA486.T0 AA492.T1 AA492.T3 AA495.T0 AA495.T1 AA495.T2 AA495.T3 AA499.T0 AA534.T0 AA539.T0 AA543.T2 AA543.T3 AA549.T1 AA549.T2 AA549.T3 AA550.T1 --hemi rh --meas thickness --tablefile rh.aparc.thick.txt The message came: SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files ERROR: The stats file /opt/freesurfer/subjects/AA471.T1/stats/rh.aparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files

I used the skip option only to find this message SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the .stats files Skipping /opt/freesurfer/subjects/AA471.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA471.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA471.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA474.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA476.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA479.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA483.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA486.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA492.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA492.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA495.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA499.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA534.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA539.T0/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA543.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA543.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T1/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T2/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA549.T3/stats/rh.aparc.stats Skipping /opt/freesurfer/subjects/AA550.T1/stats/rh.aparc.stats Building the table.. Traceback (most recent call last): File "/opt/freesurfer/bin/aparcstats2table", line 338, in <module> rows, columns, table = sanitize_table(options, pretable) File "/opt/freesurfer/bin/aparcstats2table", line 253, in sanitize_table _spec, _parc_measure_map = dt[0] IndexError: list index out of range

Please advise. Rashmi.

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