External Email - Use Caution        

 
I believe the assumption is the freesurfer 7.3.1 distribution has already been installed (under /usr/local/freesurfer/7.3.1 by the *.deb or *.rpm linux installer file) and that FREESURFER_HOME is set in the environment  (/usr/local/freesurfer/7.3.1).  You should be able to download and run the 7.3.1 freesurfer installer using one of the 7.3.1 links from https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads.

After running the freesurfer installer, the steps - which it looks like you are already using - are listed below from a bash terminal window,

$ export FREESURFER_HOME=/usr/local/freesurfer/7.3.1

$ cd  $FREESURFER_HOME/bin

.... you can try using either R2019b or R2014b ...

$ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b

I'm not sure the paths generated by the Maltab installer for use in LD_LIBRARY_PATH are always the same.   They may not be if it uses some temporary path naming mechanism.  So you may need to capture the output from the matlab installer, parse out the LD_LIBRARY_PATH setting each time it is run, and set it in the environment.

- R.

On 12/6/23 13:58, Na, Xiaoxu (XNA@uams.edu) wrote:

        External Email - Use Caution        

Dear Freesurfer Experts,

 

I’m building a docker file with freesurfer and matlab run time. May I know if freesurfer 7.3.1 should be compatible with matlab run time 2019b?

If so, what else can I make the environment setting correct in order to run localGI?

 

I tried to run “cd $FREESURFER_HOME/bin && sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b” and it finished successfully and I also appended the “/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so” to  "$LD_LIBRARY_PATH".

 

On the target computer, append the following to your LD_LIBRARY_PATH environment variable:

 

/tmp/tmp.T0m3Pxj9fW/install-target/v97/runtime/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/bin/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/sys/os/glnxa64:/tmp/tmp.T0m3Pxj9fW/install-target/v97/extern/bin/glnxa64

 

If MATLAB Runtime is to be used with MATLAB Production Server, you do not need to modify the above environment variable.

 

(Dec 06, 2023 17:26:10) Exiting with status 0

(Dec 06, 2023 17:26:10) End - Successful.

Finished

R2019b installed successfully in /opt/freesurfer-7.3.1/MCRv97

Removing intermediate container afe25e3801f1

---> ae8788b3fa89

Step 13/14 : ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so

---> Running in e3601f8c33c4

Removing intermediate container e3601f8c33c4

---> 404199efd51a

Step 14/14 : RUN echo "$LD_LIBRARY_PATH"

---> Running in ac3754cb24bb

:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv94/bin/glnxa64/libmwlaunchermain.so

Removing intermediate container ac3754cb24bb

---> 9e9c3e2e0051

Successfully built 9e9c3e2e0051

 

 

However, when I run “recon-all -s BL-101 -localGI” on the subject BL-101 that was successfully finished was recon-all previously, it yelled Malab was not available. Could you please help where I did wrong? Thank you so much!

 

start

/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv97/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv97/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv97/bin/glnxa64/libmwlaunchermain.so:/.singularity.d/libs

recon-all -s BL-101 -localGI

fs-check-version --s BL-101 --o /tmp/tmp.rbqOyn

Wed Dec  6 18:51:08 UTC 2023

 

setenv SUBJECTS_DIR /home/xna/fmri/data_BF_str

cd /home/xna/fmri/data_BF_str

/opt/freesurfer-7.3.1/bin/fs-check-version --s BL-101 --o /tmp/tmp.rbqOyn

-rwxrwxr-x 1 root root 18565 Dec  6 17:50 /opt/freesurfer-7.3.1/bin/fs-check-version

 

freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466

$Id$

Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

pid 106796

Current FS Version freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466

bstampfile exists /home/xna/fmri/data_BF_str/BL-101/scripts/build-stamp.txt

Subject FS Version: freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466

No constraints on version because REQ=UnSet and FsVerFile=NotThere

#@#% fs-check-version match = 1

fs-check-version Done

INFO: SUBJECTS_DIR is /home/xna/fmri/data_BF_str

Actual FREESURFER_HOME /opt/freesurfer-7.3.1

-rw-rw-r-- 1 xna xna 1158857 Dec  6 18:24 /home/xna/fmri/data_BF_str/BL-101/scripts/recon-all.log

Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

~/fmri/data_BF_str/BL-101/mri/transforms ~/fmri/data_BF_str/BL-101

~/fmri/data_BF_str/BL-101

#@# white curv lh Wed Dec  6 18:51:09 UTC 2023

cd /home/xna/fmri/data_BF_str/BL-101/mri

mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv

   Update not needed

#@# white area lh Wed Dec  6 18:51:09 UTC 2023

cd /home/xna/fmri/data_BF_str/BL-101/mri

mris_place_surface --area-map ../surf/lh.white ../surf/lh.area

   Update not needed

#@# pial curv lh Wed Dec  6 18:51:09 UTC 2023

cd /home/xna/fmri/data_BF_str/BL-101/mri

mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial

   Update not needed

#@# pial area lh Wed Dec  6 18:51:09 UTC 2023

cd /home/xna/fmri/data_BF_str/BL-101/mri

mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial

   Update not needed

#@# thickness lh Wed Dec  6 18:51:09 UTC 2023

cd /home/xna/fmri/data_BF_str/BL-101/mri

mris_place_surface --thickness ../surf/lh.white .../surf/lh.pial 20 5 ../surf/lh.thickness

   Update not needed

#@# area and vertex vol lh Wed Dec  6 18:51:09 UTC 2023

cd /home/xna/fmri/data_BF_str/BL-101/mri

mris_place_surface --thickness ../surf/lh.white .../surf/lh.pial 20 5 ../surf/lh.thickness

   Update not needed

#@# white curv rh Wed Dec  6 18:51:09 UTC 2023

cd /home/xna/fmri/data_BF_str/BL-101/mri

mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv

   Update not needed

#@# white area rh Wed Dec  6 18:51:09 UTC 2023

cd /home/xna/fmri/data_BF_str/BL-101/mri

mris_place_surface --area-map ../surf/rh.white ../surf/rh.area

   Update not needed

#@# pial curv rh Wed Dec  6 18:51:09 UTC 2023

cd /home/xna/fmri/data_BF_str/BL-101/mri

mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial

   Update not needed

#@# pial area rh Wed Dec  6 18:51:09 UTC 2023

cd /home/xna/fmri/data_BF_str/BL-101/mri

mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial

   Update not needed

#@# thickness rh Wed Dec  6 18:51:09 UTC 2023

cd /home/xna/fmri/data_BF_str/BL-101/mri

mris_place_surface --thickness ../surf/rh.white .../surf/rh.pial 20 5 ../surf/rh.thickness

   Update not needed

#@# area and vertex vol rh Wed Dec  6 18:51:09 UTC 2023

cd /home/xna/fmri/data_BF_str/BL-101/mri

mris_place_surface --thickness ../surf/rh.white .../surf/rh.pial 20 5 ../surf/rh.thickness

   Update not needed

/home/xna/fmri/data_BF_str/BL-101/surf

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

#@# Local Gyrification Index lh Wed Dec  6 18:51:09 UTC 2023

 

mris_compute_lgi --i lh.pial

 

ERROR: Matlab is required to run mris_compute_lgi!

Linux xbt088 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

 

recon-all -s BL-101 exited with ERRORS at Wed Dec  6 18:51:09 UTC 2023

 

For more details, see the log file /home/xna/fmri/data_BF_str/BL-101/scripts/recon-all.log

To report a problem, see MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

 

Regards,

Xiaoxu

 

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