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 <schummanr@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.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

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