Hello K, If you type
$ asegstats2table --help you will see that you can specify subjects on the command line as, e.g., for bert as —subjects bert or apparently -s bert It looks like the subjects option expects the name for at least one subjects (data), but the help output says you can list more than one subjects name as the argument to —subjects On Aug 12, 2018, at 12:31 PM, Schumman Resonance <schumm...@gmail.com<mailto:schumm...@gmail.com>> wrote: External Email - Use Caution Hi, I'm trying to run the Stats2table_bash.sh script from Jamaan Alghamdi & Dr. Vanessa Sluming. And I get This error: File "/Applications/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/Applications/freesurfer/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' ^ SyntaxError: invalid syntax File "/Applications/freesurfer/bin/aparcstats2table", line 156 print 'ERROR: atleast 1 subject must be provided' . . . This is my set up: _________________________________________________________________ -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/schumman/data MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl _________________________________________________________________ This is the line from SetUpFreeSurfer.sh for my subjects directory ____________________________________________________________ # Set this to your subjects/ dir, usually freesurfer/subjects/ if [ -z $SUBJECTS_DIR ]; then export SUBJECTS_DIR=/Users/schumman/data __________________________________________________ And I modified in their script to my FREESURFER_HOME as below #!/bin/bash path=`dirname $0` sleep 1 cd $path echo "This bash script will create table from ?.stats files" echo "Written by Jamaan Alghamdi & Dr. Vanessa Sluming" echo "University of Liverpool" echo "jamaan.algha...@gmail.com<mailto:jamaan.algha...@gmail.com>" echo "http://www.easyneuroimaging.com<http://www.easyneuroimaging.com/>" echo "20/12/2010 " export FREESURFER_HOME=/Applications/freesurfer sleep 1 source $FREESURFER_HOME/SetUpFreeSurfer.sh sleep 1 export SUBJECTS_DIR=$PWD list="`ls -d */`" asegstats2table --subjects $list --meas volume --skip --statsfile wmparc.stats --all-segs --tablefile wmparc_stats.txt . . . I run the script from my_subject_directory. I suspect this is something very obvious I'm not able to see and I apologize for such a basic question, any help would be much appreciated. Thanks, K _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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