eduardklap
commented
6 years ago Dear Jamie, Thanks for trying out our tool and reporting these problems! Hope I can help a bit, because these issues are more specific for FreeSurfer / stats2table. Most important thing is that for the Qoala-T tool the specific aseg/aparc files as listed in stats2table_bash_qoala_t.sh are needed.
It might be there useful to add a fuller call to the stats2table_bash_qoala_t.sh call (e.g., python2 $FREESURFER_HOME/bin/asegstats2table).
Good point, will add this as a possible solution. On my system it does work with python 3.5.2 however, so I wouldn't recommend it as a standard solution.
*** Also, my asegstats2table doesn't take hemisphere-based option calls. If I now try, python2 $FREESURFER_HOME/bin/asegstats2table --subjects $list --hemi lh --meas volume --skip --tablefile aparc_volume_lh.txt
I got this error asegstats2table: error: no such option: --hemi
The error here is because you used asegstats2table, but it must be aparcstats2table I think: python2 $FREESURFER_HOME/bin/aparcstats2table --subjects $list --hemi lh --meas volume --skip --tablefile aparc_volume_lh.txt
Hope this works! Let us know if you run into any other problems.
Best, Eduard
Hello Drs. Wierenga & Klapwijk (and other Qoala-T users),
I just wanted to send a quick note regarding potentially specifying the python version stats2table_bash_qoala_t.sh. I tried to run that script right after cloning the repo, but got this error (note: I just made the path a $1 variable to specify after the sh call)--
jamielh@pfc:~/Volumes/Hanson/Neuroimaging_Resources/Qoala-T$ ./stats2table_bash_qoala_t.sh /home/jamielh/Volumes/Hanson/Duke_PAC/proc/Freesurfer This bash script will create table from ?.stats files Written by Jamaan Alghamdi & Dr. Vanessa Sluming University of Liverpool jamaan.alghamdi@gmail.com http://www.easyneuroimaging.com 20/12/2010
File "/usr/local/pkg/freesurfer//bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/usr/local/pkg/freesurfer//bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(print 'ERROR: atleast 1 subject must be provided')? File "/usr/local/pkg/freesurfer//bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(print 'ERROR: atleast 1 subject must be provided')? File "/usr/local/pkg/freesurfer//bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(print 'ERROR: atleast 1 subject must be provided')? File "/usr/local/pkg/freesurfer//bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(print 'ERROR: atleast 1 subject must be provided')? File "/usr/local/pkg/freesurfer//bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(print 'ERROR: atleast 1 subject must be provided')? File "/usr/local/pkg/freesurfer//bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(print 'ERROR: atleast 1 subject must be provided')?
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Some googling on the Freesurfer list noted that there are sometimes issues with Python version of folks system (i.e., Python 2 v. 3 don't play well together). See this link.
It might be there useful to add a fuller call to the stats2table_bash_qoala_t.sh call (e.g., python2 $FREESURFER_HOME/bin/asegstats2table).
*** Also, my asegstats2table doesn't take hemisphere-based option calls. If I now try,
python2 $FREESURFER_HOME/bin/asegstats2table --subjects $list --hemi lh --meas volume --skip --tablefile aparc_volume_lh.txtI got this error
asegstats2table: error: no such option: --hemiI think I have the newest version of Freesurfer (but I'm not 100% about that). Thoughts on how to tackle that issue? I'm still working through things, but thanks for the tool development. Looks promising.
Best, Jamie.