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-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
 

        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 <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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer