Hi Xiaoxu,
This is how I built a FreeSurfer 7.1.1 container with matlabmcr 2014b
(https://github.com/pwighton/fs-docker/blob/master/notes/20201127-fs711-neurodocker-min.md#freesurfer711)
```
neurodocker generate docker \
--base continuumio/miniconda:4.7.12 \
--pkg-manager apt \
--freesurfer version=7.1.1 \
--matlabmcr version=2014b install_path=/opt/MCRv84 \
--run "ln -s /opt/MCRv84/v84 /opt/freesurfer-7.1.1/MCRv84" \
| docker build -t pwighton/freesurfer:7.1.1 -
```
I had to create a symlink from /opt/freesurfer-7.1.1/MCRv84 to /opt/MCRv84/v84
You could try to see if 7.3.1 works with matlabmcr 2014b, or update the symlink
accordingly for 2019b.
Hope this helps!
-Paul
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Na, Xiaoxu <x...@uams.edu>
Sent: Thursday, December 7, 2023 11:23 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b
External Email - Use Caution
Thank you for your information! However, even though I appended the temporary
paths that were generated right after running mcr installation. While running,
I first printed out the $ LD_LIBRARY_PATH, it seems right. However, the same
error occurred. I didn’t install the freesurfer in the default folder, if that
may be a problem. I used neurodocker to build the base image with freesurfer
7.3.1 running correctly. Is there anything else I can try? Thank you so much!
Regards,
Xiaoxu
:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-7.3.1/MCRv84/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv84/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv84/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv84/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv84/bin/glnxa64/libmwlaunchermain.so:/usr/lib/x86_64-linux-gnu/:opt/freesurfer-7.3.1/MCRv84/runtime/glnxa64:/opt/freesurfer-7.3.1/MCRv84/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv84/sys/os/glnxa64:/opt/freesurfer-7.3.1/MCRv84/extern/bin/glnxa64:/opt/freesurfer-7.3.1/MCRv84/bin/glnxa64/libmwlaunchermain.so:/tmp/tmp.s91tLX1Jfv/install-target/v84/runtime/glnxa64:/tmp/tmp.s91tLX1Jfv/install-target/v84/bin/glnxa64:/tmp/tmp.s91tLX1Jfv/install-target/v84/sys/os/glnxa64::/.singularity.d/libs
recon-all -s BL-101 -localGI
fs-check-version --s BL-101 --o /tmp/tmp.UQALDw
Thu Dec 7 15:57:37 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.UQALDw
-rwxrwxr-x 1 root root 18565 Dec 7 15:31
/opt/freesurfer-7.3.1/bin/fs-check-version
freesurfer-linux-centos7_x86_64-7.3.1-20220723-115e466
$Id$
Linux xbt090 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 107005
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 1220527 Dec 7 13:57
/home/xna/fmri/data_BF_str/BL-101/scripts/recon-all.log
Linux xbt090 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 Thu Dec 7 15:57:43 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 Thu Dec 7 15:57:43 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 Thu Dec 7 15:57:43 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 Thu Dec 7 15:57:43 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 Thu Dec 7 15:57:43 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 Thu Dec 7 15:57:43 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 Thu Dec 7 15:57:43 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 Thu Dec 7 15:57:43 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 Thu Dec 7 15:57:43 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 Thu Dec 7 15:57:43 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 Thu Dec 7 15:57:43 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 Thu Dec 7 15:57:43 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 Thu Dec 7 15:57:43 UTC 2023
mris_compute_lgi --i lh.pial
ERROR: Matlab is required to run mris_compute_lgi!
Linux xbt090 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 Thu Dec 7 15:57:43 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<http://secure-web.cisco.com/19z1ocn0OehHUGM4w6oiRnM6yr0UPgIGAZZxoya2UA2h4t8qi3-4qexKM59ajGsfrz7ib2U-SrmLHQdZJ95lZCAh6je5ny8UGsLOCbTJfwlv4NNCaud1J9PTBFJIAf6fW-q6Qgg-yyITcS1to7QYk6f6PkiT03tcV2wNsk_BYRJNamVMXwWfk427kOpr4mvddtzytLtss89btV4-SAEEA4n8ZVZadouTkCPGoFwXBjaixaBlKWkEl8J5An4a_s_aT5o73DUu8To4q274fToRd8hdlWU06g8RtrlKPoRn9-6ywNGQ0STILlB1T3OybZClLJ8DmyLCc4Z_ri49pguBC_g/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting>
finish
From: fsbuild <fsbu...@contbay.com<mailto:fsbu...@contbay.com>>
Sent: Wednesday, December 6, 2023 9:14 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Cc: Na, Xiaoxu <x...@uams.edu<mailto:x...@uams.edu>>
Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b
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).
ZjQcmQRYFpfptBannerStart
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This message came from outside your organization.
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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 MailScanner has
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be
https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads<https://secure-web.cisco.com/1M-gFnrnIJ-MOUpvREJw-JKitdgCKNA8aJw4B8Vg7lSCrwCLGKEux7EtwgiJMp3QQtgfuvSlzRJnFoOZo2PHM6a5WQzzITo6Vria4FgoDzsVgWzSwo-AxFOErH4zcGZ2_TNatyiGM7Mz_9wlFpbwIU7iK0g3_m5SXIPireLMIyiIC6r_20LFeiLyHMIha1AlqkevZZbMf7vXhTSqu_8KzxtoIVo3hrPSZQKeZ6O2NaKoz9PgqeiLeSTU2fVx4uyGRn6nVL8rBRf2m22BiLQlcjGA7BWqrQuG0XVZRWRv6hKAVRM6lbSD1wEF_uSOTmgI17hQDQYuH4PGtjNrQtU8v6A/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads__%3B%21%21LFqOYw%21tDBZFrn3IUiIYFmlM2uL6_tGbVoPuNqWs5ClV4bXYLiasR-ZsSbQP2scMUQqGzU2mRnDo0R9cUG3gw%24>.
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 (x...@uams.edu<mailto:x...@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<https://secure-web.cisco.com/1hvYCCErje-MUOn9IgzcBShRONns5bVbUWgfe-ybvxkeCQa2gIQlOS_2ObCm5I_CEqVuEeu5EqMfmd2ItEpPJTOED7VMKPdA0H-auEU39CBYG_vsAkS0JPR1dM3AdH7iKUu9ncN7HDb-C_Yhd1U1phTFbp6VPbH1W9s9-DqLs9ZGPkS-S-0ZoIz3m4ic0fzlAelfRc2xzP8EwgcmvjYSWDi5D8XrNVJEjEZmQSgPW2prZhibd6zS6ZgXNT11sS5ldkYUB3ppsF3-oeAlvHQwnylP55vYsgL1tP2OKAKIuuMfz9PxQXlQPRYm5A34M-WKlB3yLxLo7EAxfeBq2RL9OKQ/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsecure-web.cisco.com%2F10JlU9uC5Jx9CmqgAZa_0KlYFqyorcNvk6q66KAYmJMeQk0FWzT50gXlpuJkzmflxujtyczft13iy1XlOsnHw9vCdbPpJzZrFOkTwiHQIKrSROUzKEapekUE0bsof4vjHK6hzapTNYGUJbnCUhb96MU1CAzIIdcwOg8F43bQwQvv0pilp_XFiQaxLHxHFzLbGYvtNgtL9WDqIKUjWvgyukrpDnn9kSofIMacyRam-0lR-DUibGnJCvrSDTY39dWzv9snNTd5fuCwhzy8sPZ2aDHWylixcOqsfDozqooHqmvEUC6g--w6PkIMMFaVgjl3A%2Fhttp%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2FBugReporting__%3BJSUlJSU%21%21LFqOYw%21tDBZFrn3IUiIYFmlM2uL6_tGbVoPuNqWs5ClV4bXYLiasR-ZsSbQP2scMUQqGzU2mRnDo0TdfS4yFw%24>
Regards,
Xiaoxu
________________________________
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