Did you look at the file to see if it looks reasonable? Eg, it might be completely empty if you ran out of space during the processing. doug
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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