Stats2table_bash.sh script

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Schumman Resonance

12 Aug 2018 12 Aug '18

12:31 p.m.

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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.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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Dicamillo, Robert

12 Aug 12 Aug

4:26 p.m.

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.commailto: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:

This is my set up:

_________________________________________________________________

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.commailto:jamaan.alghamdi@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.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Dicamillo, Robert

5:03 p.m.

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.commailto: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:

This is my set up:

_________________________________________________________________

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.commailto:jamaan.alghamdi@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

Schumman Resonance

7:03 p.m.

External Email - Use Caution

Thanks Robert, I guess my main issue is that I don't fully understand how the script works:

[1] export SUBJECTS_DIR=*$PWD* *[2] list="`ls -d */`"* [3] asegstats2table --subjects *$list *--meas volume --skip --statsfile wmparc.stats --all-segs --tablefile wmparc_stats.txt

I was assuming the variable $list would give SUBJECTS to --subjects based on each directory where .stats files are. I don't fully understand how lines [1] and [2] work.

Apologies if I'm not conveying my struggle with proper coding language :)

On Sun, Aug 12, 2018 at 2:03 PM, Dicamillo, Robert < RDICAMILLO@mgh.harvard.edu> wrote:

...

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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Hoopes, Andrew

13 Aug 13 Aug

3:47 p.m.

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

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:

This is my set up:

_________________________________________________________________

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.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

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Dicamillo, Robert
Hoopes, Andrew
Schumman Resonance