asegstats2table is a python2 script, and you are likely running it with python3. Try running the script with “python2” prepended to the command:
python2 asegstats2table --subjects $list --meas volume --skip --statsfile wmparc.stats --all-segs --tablefile wmparc_stats.txt best, Andrew From: <[email protected]> on behalf of Schumman Resonance <[email protected]> Reply-To: FS Help <[email protected]> Date: Sunday, August 12, 2018 at 12:33 PM To: FS Help <[email protected]> Subject: [Freesurfer] Stats2table_bash.sh script 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 "[email protected]<mailto:[email protected]>" echo "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
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