Dear Ola,
This looks like a very ugly error but someone experienced something similar in the past and it turned out to be a permissions problem.
Can you please double check this is not your case?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Olamide Abiose <oabiose@stanford.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, 10 October 2019 at 14:29
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Issues with segmentHA_T1.sh command
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