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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