Hi Mamun,

There is a little bug in the script.

I’ll fix the dev version ASAP, but rather than downloading a gigabyte, I’d suggest that you simply edit quantifyHAsubregions.sh (found in $FREESURFER_HOME/bin/) and replace these two lines:

  leftVolFile="$resultsDirectory/$subjectName/mri/lh.${suffix}Volumes-${suffix}.v20.txt"

  rightVolFile="$resultsDirectory/$subjectName/mri/rh.${suffix}Volumes-${suffix}.v20.txt"

by:

  leftVolFile="$resultsDirectory/$subjectName/mri/lh.${prefix}Volumes-${suffix}.v20.txt"

  rightVolFile="$resultsDirectory/$subjectName/mri/rh.${prefix}Volumes-${suffix}.v20.txt"

Cheers,

/Eugenio

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Md. Mamun Al-Amin" <mdalaminbadal@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, 17 September 2017 at 03:46
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Hippocampal subfield segmentation error

Hi Eugenio

Thanks for your attention.

I solved this problem today. I found two JAVA versions in my macbook (Library/Java/JavaVirtualMachines). I think they were conflicting. So I deleted latest java folder.

By the way, I have been trying to gather the volume analyzed from all subjects. However, it is not working.

I used following command
quantifyHAsubregions.sh amygNuc T1 amyg.txt /Volumes/mamun/CB_Long/

However I found nothing in my CB_Long directory.

Would you please help me solving this issue?

On Sun, Sep 17, 2017 at 7:26 AM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:

Dear MMAA,

That looks like a runtime error. Did you have any problems with version 6.0?

Cheers,

/Eugenio

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Md. Mamun Al-Amin" <mdalaminbadal@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, 15 September 2017 at 00:54
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampal subfield segmentation error

Dear Experts

I have been experiencing a problem while running the following command

segmentHA_T1.sh subject_name

The program exits with the following error

"MATLAB is exiting because of fatal error
/Applications/freesurfer-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 39:   660 Killed: 9               "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args"

The log file is attached herewith.

I have reinstalled Matlab R2012 runtime. However, still I am experiencing same problem.

Looking for a solution.

I would appreciate your suggestion.

--

Kind regards

Md. Mamun Al-Amin

------------------------------

PhD Candidate, Queensland Brain Institute

Building 79, St Lucia QLD 4072

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--

Kind regards

Md. Mamun Al-Amin

------------------------------

PhD Candidate, Queensland Brain Institute

Building 79, St Lucia QLD 4072