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

---

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi Eugenio It is working. Thank you very much.

Kind regards Mamun

On Tue, Sep 19, 2017 at 7:55 AM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:

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

---

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

--

Kind regards

Md. Mamun Al-Amin

---

PhD Candidate, Queensland Brain Institute

Building 79, St Lucia QLD 4072

---

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.