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