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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 http://secure-web.cisco.com/10JlU9uC5Jx9CmqgAZa_0KlYFqyorcNvk6q66KAYmJMeQk0F...
Regards, Xiaoxu
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