External Email - Use Caution
Hi Rosalia,
I'm running this as a command line argument, because I'm only testing one
subject. Are you asking for the segmentHA_T1.sh script?
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta Aguayo
<rdacos...@gmail.com>
Sent: Thursday, October 10, 2019 2:34 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Issues with segmentHA_T1.sh command
External Email - Use Caution
Hi Olamide,
How to check your line errors without the bash script you are using?
Could you at least send the .sh script?
Best regards,
Rosalia
On Thu, Oct 10, 2019 at 8:29 PM Olamide Abiose
<oabi...@stanford.edu<mailto:oabi...@stanford.edu>> wrote:
External Email - Use Caution
Hello,
I'm having great difficulty running the segmentHA_T1.sh command. I'm using the
latest development version of Freesurfer and have downloaded Matlab R2014b. I
get the following message when I try to run the command. Any advice/suggestions
you can offer would be greatly appreciated!
Thank you very much.
#--------------------------------------------
#@# Hippocampal Subfields processing (T1) left Wed Oct 9 17:49:49 PDT 2019
/usr/bin/time -o /dev/stdout
@#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13
e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01
run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004
/mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice
0.333333333333333333333333333333333333
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz
/opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz
/opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left
L-BFGS v21 /opt/freesurfer-dev/bin/ 0
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client::
Error using checkRequiredMCRProducts (line 25)
Java exception occurred:
java.lang.NullPointerException
at
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56)
at
com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49)
at
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193)
at
com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108)
at
com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67)
Error in deployrc (line 9)
Error in matlabrc (line 238)
Command exited with non-zero status 255
@#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N
13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O
84096 L 41.67 41.74 45.01
@#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh
N 13 41.42 41.68 44.90
Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019
x86_64 x86_64 x86_64 GNU/Linux
T1 hippocampal subfields exited with ERRORS at Wed Oct 9 17:50:15 PDT 2019
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