did you try to run it outside of python? Ie,
aparcstats2table --hemi lh --subjectsfile=$(pwd)/final_list.txt -t $(pwd)/lh.test.dat --parc aparc.mapped --delimiter comma --meas thickness
On 9/24/2020 12:15 AM, Hye Min Shin wrote:
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Hello experts,
I am having trouble running aparcstats2table on a group of subjects. Everytime I run aparcstats2table I get this error:
python2 $FREESURFER_HOME/bin/aparcstats2table --hemi lh --subjectsfile=$(pwd)/final_list.txt -t $(pwd)/lh.test.dat --parc aparc.mapped --delimiter comma --meas thickness Parsing the .stats files Traceback (most recent call last): File "/usr/local/freesurfer/bin/aparcstats2table", line 376, in <module> parc_measure_map = parsed.parse(options.meas) File "/usr/local/freesurfer/bin/fsutils.py", line 215, in parse val = float(strlist[self.measure_column_map[measure]]) IndexError: list index out of range
My current freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Now I did set my SUBJECTS_DIR to the folder with subjects files. And I was able to successfully run aparcstats2table previously with other subjects.
When I ran aparcstats2table separately for a couple of subjects, it did run successfully. I thought there must be some carriage return with the text file of the list of subjects so I made sure to remove any carriage returns.
Best, Julia Shin
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