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 $args"
The log file is attached herewith.
I have reinstalled Matlab R2012 runtime. However, still I am experiencing same problem.
Looking for a solution. I would appreciate your suggestion.
Dear MMAA, That looks like a runtime error. Did you have any problems with version 6.0? Cheers, /Eugenio
-- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Md. Mamun Al-Amin" mdalaminbadal@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 15 September 2017 at 00:54 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal subfield segmentation error
Dear Experts I have been experiencing a problem while running the following command
segmentHA_T1.sh subject_name
The program exits with the following error
"MATLAB is exiting because of fatal error /Applications/freesurfer-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 39: 660 Killed: 9 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args" The log file is attached herewith. I have reinstalled Matlab R2012 runtime. However, still I am experiencing same problem.
Looking for a solution. I would appreciate your suggestion.
--
Kind regards
Md. Mamun Al-Amin ------------------------------ PhD Candidate, Queensland Brain Institute Building 79, St Lucia QLD 4072
Hi Eugenio Thanks for your attention. I solved this problem today. I found two JAVA versions in my macbook (Library/Java/JavaVirtualMachines). I think they were conflicting. So I deleted latest java folder.
By the way, I have been trying to gather the volume analyzed from all subjects. However, it is not working. I used following command
*quantifyHAsubregions.sh amygNuc T1 amyg.txt /Volumes/mamun/CB_Long/*
However I found nothing in my CB_Long directory.
Would you please help me solving this issue?
On Sun, Sep 17, 2017 at 7:26 AM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:
Dear MMAA,
That looks like a runtime error. Did you have any problems with version 6.0?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Md. Mamun Al-Amin" mdalaminbadal@gmail.com *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, 15 September 2017 at 00:54 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Hippocampal subfield segmentation error
Dear Experts
I have been experiencing a problem while running the following command
*segmentHA_T1.sh subject_name*
The program exits with the following error
"MATLAB is exiting because of fatal error /Applications/freesurfer-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 39: 660 Killed: 9 "${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 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.ukmailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Md. Mamun Al-Amin" <mdalaminbadal@gmail.commailto:mdalaminbadal@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 15 September 2017 at 00:54 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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
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-${ suffix}.v20.txt"
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Md. Mamun Al-Amin" mdalaminbadal@gmail.com *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Sunday, 17 September 2017 at 03:46 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Hippocampal subfield segmentation error
Hi Eugenio
Thanks for your attention.
I solved this problem today. I found two JAVA versions in my macbook (Library/Java/JavaVirtualMachines). I think they were conflicting. So I deleted latest java folder.
By the way, I have been trying to gather the volume analyzed from all subjects. However, it is not working.
I used following command
- quantifyHAsubregions.sh amygNuc T1 amyg.txt /Volumes/mamun/CB_Long/*
However I found nothing in my CB_Long directory.
Would you please help me solving this issue?
On Sun, Sep 17, 2017 at 7:26 AM, Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:
Dear MMAA,
That looks like a runtime error. Did you have any problems with version 6.0?
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Md. Mamun Al-Amin" mdalaminbadal@gmail.com *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, 15 September 2017 at 00:54 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] Hippocampal subfield segmentation error
Dear Experts
I have been experiencing a problem while running the following command
*segmentHA_T1.sh subject_name*
The program exits with the following error
"MATLAB is exiting because of fatal error /Applications/freesurfer-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 39: 660 Killed: 9 "${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.
freesurfer@nmr.mgh.harvard.edu