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: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Schumman Resonance schummanr@gmail.com Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Sunday, August 12, 2018 at 12:33 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Stats2table_bash.sh script
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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:
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-------- 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
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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
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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.alghamdi@gmail.commailto:jamaan.alghamdi@gmail.com" 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