Thank you.  That seemed to work.

 

Best,

 

 

 

Hi Ali,

 

Can you please remove the MCR directory and install it using the instructions found at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime? I think this will fix the issue.

 

Best,

Andrew

 

        External Email - Use Caution        

Hello,

 

I’m helping a user run freesurfer/7.1.0 on CentOS 8.1.  They initially encountered an error due to the missing Matlab Compiler Runtime (MCR).  I downloaded the package and installed it in the location suggested by the error message :

 

LINUX:

 

cd /gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download

curl "MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2014bLinux.tar.gz" -o "runtime2014b.tar.gz"

tar xvf runtime2014b.tar.gz

 

After installing the MCR, I had to change all the subdirectories’ in MCRv84 to 755 permissions so our user could access it.   When trying to run `segmentHA_T1.sh`, she gets the error :

 

[user@computer-name Subjects]$ export FS_LICENSE=/gpfs0/home1/group/lab/Software/FreeSurfer/license.txt

[user@computer-name Subjects]$ export SUBJECTS_DIR=/gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects

[user@computer-name Subjects]$ cd /gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects

[user@computer-name Subjects]$ segmentHA_T1.sh subject1

#--------------------------------------------

#@# Hippocampal Subfields processing (T1) left Wed Jan 27 10:53:02 EST 2021

------------------------------------------

Setting up environment variables

---

LD_LIBRARY_PATH is .:/lib64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//runtime/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//bin/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/os/glnxa64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/server:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64/client:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/MCRv84//sys/java/jre/glnxa64/jre/lib/amd64:/gpfs0/export/apps/opt/freesurfer/7.1.0/binary_download/lib:/gpfs0/export/apps/easybuild/software/binutils/2.34-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/zlib/1.2.11-GCCcore-9.3.0/lib:/gpfs0/export/apps/easybuild/software/GCCcore/9.3.0/lib64:/gpfs0/export/apps/easybuild/software/GCCcore/9.3.0/lib

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  2021:01:27:10:53:02 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 35.91 S 0.42 U 2.80 P 8% M 184232 F 0 R 52021 W 0 c 11 w 7851 I 0 O 84128 L 0.02 0.06 0.08

@#@FSLOADPOST 2021:01:27:10:53:38 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 0.35 0.15 0.11

Linux computer-name 4.18.0-147.el8.x86_64 #1 SMP Wed Dec 4 21:51:45 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

 

T1 hippocampal subfields exited with ERRORS at Wed Jan 27 10:53:38 EST 2021

 

For more details, see the log file /gpfs0/home1/group/lab/DATA/ANALYSES/Test/FreeSurfer7/Subjects/subject1/scripts/hippocampal-subfields-T1.log

 

In the archive, it seems that this has been encountered before (here and there).  Unfortunately the only solution is to ‘fix the permissions’ without specifying which files and to what permissions.

 

 

Question:

1. Is there any resolution to this issue?

2. Is the Matlab 2014b compatible with CentOS 8.1?

 

Best regards,