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?

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta Aguayo <rdacostaa@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

 

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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 <oabiose@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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