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: <[email protected]> on behalf of "Md. Mamun Al-Amin"
<[email protected]>
Reply-To: Freesurfer support list <[email protected]>
Date: Sunday, 17 September 2017 at 03:46
To: Freesurfer support list <[email protected]>
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
<[email protected]<mailto:[email protected]>> 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:
<[email protected]<mailto:[email protected]>>
on behalf of "Md. Mamun Al-Amin"
<[email protected]<mailto:[email protected]>>
Reply-To: Freesurfer support list
<[email protected]<mailto:[email protected]>>
Date: Friday, 15 September 2017 at 00:54
To: Freesurfer support list
<[email protected]<mailto:[email protected]>>
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
_______________________________________________
Freesurfer mailing list
[email protected]
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.
