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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:
_________________________________________________________________
-------- 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"
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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