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Thank you Paul! But I have already updated my neurodocker to the latest. I’ve tried to create a link using the same way you’ve listed below, and it didn’t help. In this way, I feel the mcr was not fully installed as I couldn’t locate the file MCRv97/bin/glnxa64/libmwlaunchermain.so, that’s why I turned to the official way, which installed a lot more files in that directory, but still not working.

The official way that R suggested, I feel like the script fs_install_mcr has already remove the temp it created during the installation once exit, so appending that to $LD_LIBRARY_PATH didn’t help. Any other tricks? Thanks so much!

Regards, Xiaoxu

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Wighton, Paul Sent: Thursday, December 7, 2023 10:35 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

Hi Xiaoxu, This is how I built a FreeSurfer 7. 1. 1 container with matlabmcr 2014b (https: //urldefense. com/v3/__https: //github. com/pwighton/fs-docker/blob/master/notes/20201127-fs711-neurodocker-min. md*freesurfer711__;Iw!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g$) ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd

Hi Xiaoxu,

This is how I built a FreeSurfer 7.1.1 container with matlabmcr 2014b

(https://secure-web.cisco.com/1stEaYfnGKKfzRhk5IPdDU1l5J1MLIxrqeEZ5yzHm2M9kIS...https://secure-web.cisco.com/1VU8fobdt3ltIdBwd_RKxm6UFQ_72eMkTDjyJn7hscwSEM2Z098eziq_jSNPVJ2xBO02l42pNukPRyyuCsgeEvT582wmRxxMtKF_cZSLATxb5hphRyeNM8S_1zSSFAoXop-sIaEuP6CIjKLSfFaRZBeKP7ohLg4LkqKt3GE_AED0O-opGxh6T-vHZCIjr_-pIfBqtgN0B_BitXE6DWPM6jiqRGKCApJcy_HHT-pWfq2tOaf9eDgeQUnhS_Cy7K2Im3rU5MOatFrqZSoRiPOi6UFpCmAJwyP83U8pIkNm07-EwY5yI0TrmkwLNvLRl3C8xnqlSFM7TZNQWIztyOGGuWw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fgithub.com%2Fpwighton%2Ffs-docker%2Fblob%2Fmaster%2Fnotes%2F20201127-fs711-neurodocker-min.md*freesurfer711__;Iw!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g$)

```

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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Na, Xiaoxu <XNA@uams.edumailto:XNA@uams.edu>

Sent: Thursday, December 7, 2023 11:23 AM

To: Freesurfer support list

Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

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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 https://secure-web.cisco.com/1P1Sx_CXam4G-ZiA_fLeX5UBTV1Q5c41v2GNqToHGIKsv9T...https://secure-web.cisco.com/13aAEnEvMFkrNpQUjzvDbvUycMGbG3TKo48iY8uyGt7-MKfI1B210QP3iuYAdAju3-cHDe2OOE3suiadB7vsNv0Rm8nPO7MqZcL0F0E3I7CGeqNgR2WuhNfUYs7qG-xWObvo7_dDNCH67N0kMeaUgcOy1iNeS_sp2HnvpiW9I58lJs3sBlLg-JsbybFdk1ljURutA2MdOMKfGu4JBrPAm-vn93xxG6N0W_RuE0ZwSaWmvmxAh8plbtLci43NEKMUVDq1UX3qvaP70iUDT5HFUsH5BoaCOWbrDMM7yALccqcMZ-J3ya_cixkZyj6VBqXEfBjvRIdn2FmNUPaFVGJ50VA/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting__;!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA$<https://secure-web.cisco.com/1Sn7T3U5IXl4qYcbixEUJcb-Khm7St9s7j7LlNMOnj_L1Ot...https://secure-web.cisco.com/1maAeQ_cFQEtGsd065BHys--zoBmjm8-pG4ZrhyXk_O54rks4fS0RvmlTZqg5mh37303HBnRrBhDEvcrnMl5Mrlrd6OziADO3zuUTQcy28SjUzwBeJt5o6wYguIi9XABbwx9tf0-ECfzHtNj0hyQwUCqep30dB9R93UsvRpTGY-rpgBVxCsdwo7aIFaUTC2Wba3K51y_lYLXjRGRt3W4MJ2Uv2KInI-O9--Ix1I001PWPgL9VCQdcjsjlaQ7Ti-6Nugznj8fTIwrbR5NuEn4uF7sJT1f9wFG7Ot3ScewZySpKFO5iazk9qufU4fWIWE_31ZbwXOclnIHgGDqW6lBFpA/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsecure-web.cisco.com%2F19z1ocn0OehHUGM4w6oiRnM6yr0UPgIGAZZxoya2UA2h4t8qi3-4qexKM59ajGsfrz7ib2U-SrmLHQdZJ95lZCAh6je5ny8UGsLOCbTJfwlv4NNCaud1J9PTBFJIAf6fW-q6Qgg-yyITcS1to7QYk6f6PkiT03tcV2wNsk_BYRJNamVMXwWfk427kOpr4mvddtzytLtss89btV4-SAEEA4n8ZVZadouTkCPGoFwXBjaixaBlKWkEl8J5An4a_s_aT5o73DUu8To4q274fToRd8hdlWU06g8RtrlKPoRn9-6ywNGQ0STILlB1T3OybZClLJ8DmyLCc4Z_ri49pguBC_g%2Fhttp*3A*2F*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FBugReporting__;JSUlJSU!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNRBpyMWeg$>

finish

From: fsbuild <fsbuild@contbay.com<mailto:fsbuild@contbay.commailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com>>

Sent: Wednesday, December 6, 2023 9:14 PM

To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu>

Cc: Na, Xiaoxu <XNA@uams.edu<mailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto:XNA@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).

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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://secure-web.cisco.com/1xOIKvRbUi4ohEnpThxPWie6S6JJpZUbIUz9ZWZHIrQJRGK...https://secure-web.cisco.com/1M6Ts-a6qEp8dfNRq5HLywV8fD-7bOYjLVtqDOr2VYAZ2twTFl1yIJiWWaxn-J_8l1R7so1TiaXknvwFylXYFmtqrX7fmQbwDvxmXOdHblAkLzibt2wqTrChLv0t-KiX7NtCFCyjPKgTNqPcPlM9FZFhiEFyawCLzUJNixygEyurNWPQIF1ixdm5iakExRszCy24Ne4I7UVRIQpK7mbBkEFMXRa7xqegA8_09eeFhp3fWL4S191uEEfain1FPOmmsAWEP3bW98bSLzkTvRhig3JtzefVJpOSfF8xsMMzkr01kfCW_VoYl6c9XNuPZdeEncC7ki1hePAKgRZWxuaZf3A/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads__;!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQK2zaIeA$<https://secure-web.cisco.com/1zCSyf9gdoBaH9_ItOorKY6XhrACbQdGJDCUFC7ama3glq-...https://secure-web.cisco.com/1CxPR5jahLEWK5kRY_n2MbwBYJLJyG2_V-rR8Go5mspyOz60xERi5CxG_VECW9BNs3TSJW4cSlv7Fz2-J5N5omM1z9x7ndOlOLbWCi5Odxcp5dl5VGzDIUyGWmMTqMtsDb84epQdpHh46TcFuhERHS0VElCHbM4s8ynK1R4bXRCdDYJrFqHJApsVajmyA0wtohSVyh39bu1DrC_9BXIOKlMx1iHGmeGRZSCslJM52G19VrkfdvVDrd2V0QurlYPskvXcJMfpFu5yZJpd-v4ipfs7oF501UhbRgtpGfJuYEnqTwEgvCUKuMpjdNHGQvwe-0xm8qriKijNNW7KI_d4MNw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1M-gFnrnIJ-MOUpvREJw-JKitdgCKNA8aJw4B8Vg7lSCrwCLGKEux7EtwgiJMp3QQtgfuvSlzRJnFoOZo2PHM6a5WQzzITo6Vria4FgoDzsVgWzSwo-AxFOErH4zcGZ2_TNatyiGM7Mz_9wlFpbwIU7iK0g3_m5SXIPireLMIyiIC6r_20LFeiLyHMIha1AlqkevZZbMf7vXhTSqu_8KzxtoIVo3hrPSZQKeZ6O2NaKoz9PgqeiLeSTU2fVx4uyGRn6nVL8rBRf2m22BiLQlcjGA7BWqrQuG0XVZRWRv6hKAVRM6lbSD1wEF_uSOTmgI17hQDQYuH4PGtjNrQtU8v6A%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2Frel7downloads__*3B*21*21LFqOYw*21tDBZFrn3IUiIYFmlM2uL6_tGbVoPuNqWs5ClV4bXYLiasR-ZsSbQP2scMUQqGzU2mRnDo0R9cUG3gw*24__;JSUlJSUlJSUlJSUlJSU!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNToeRruxw$>.

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<mailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto: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

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Regards,

Xiaoxu

________________________________

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External Email - Use Caution

Hi Paul,

Thank you so much for your confirmation! This is exactly what I’m having trouble with. In this case, maybe I can’t go with 7.3.1 and upper, I can go back to work with 7.1.1. Have you tried with 7.1.1 with mcrv84(matlab 2014b) running correctly? Last time I run LGI was on my own workstation with 7.1.0 and full matlab 2018b installed. Since I want to run all subjects on HPC this time, I have to build a docker to support that. If you have any version of freesurfer-mcr pair that is working for LGI, will you please kindly let me know and I’ll give it a try too? Thank you so much!

Regards, Xiaoxu

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Wighton, Paul Sent: Thursday, December 7, 2023 11:54 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

I just tried this in a container. It looks like `mris_compute_lgi` is not designed to work with the mcr, and needs a full matlab installation. I started by jumping into a freesurfer 7. 3. 1 container. ``` docker run -it --rm freesurfer/freesurfer: 7. 3. 2 ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd

I just tried this in a container. It looks like `mris_compute_lgi` is not designed to work with the mcr, and needs a full matlab installation.

I started by jumping into a freesurfer 7.3.1 container.

```

docker run -it --rm freesurfer/freesurfer:7.3.2

```

Then I installed matlab mcr

```

fs_install_mcr R2019b

```

Note the output `fs_install_mcr` says:

```

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

/tmp/tmp.AzujBUG5W7/install-target/v97/runtime/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/bin/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/sys/os/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/extern/bin/glnxa64

```

But this is what should be added to the `LD_LIBRARY_PATH`:

```

export LD_LIBRARY_PATH=${FREESURFER_HOME}/MCRv97/runtime/glnxa64:${FREESURFER_HOME}/MCRv97/bin/glnxa64:${FREESURFER_HOME}/MCRv97/sys/os/glnxa64:${FREESURFER_HOME}/MCRv97/extern/bin/glnxa64:${LD_LIBRARY_PATH}

```

And I can confirm the `mris_compute_lgi` indeed does not work:

```

mris_compute_lgi --i $FREESURFER_HOME/subjects/bert/surf/lh.pial

ERROR: Matlab is required to run mris_compute_lgi!

```

But it looks like the mcr was installed:

```

find $FREESURFER_HOME/MCRv97

```

The error is a result of `getmatlab` not being able to find the matlab binary, which isn't included in the MCR.

https://secure-web.cisco.com/13C_Y7EqlSTOB8fpUcovaIr-sNiqvYZ8-QkUp4jRzJs7m2h...https://secure-web.cisco.com/1dheVYAyGbBc3PXoP8AnQvpYdBZY6ZnMKbs7Wo41t3Dvpn7r_WStNhkXeoFxsmXr1ShbeH_UgE9uTqqw_g0-AXSsWhOLbIhKFscn1Hw95HA6CWxFyIruB7r73W-JtLh585lvsW7fUgxAUtU3u_kQH6eQrbaQFhQJC34MRBnYjiCpZv1eHvEO4Plk_hHV2KrtOMOFREhjkGQj1gPBi38E3NrUQGbOZv3C6GTJrhn7-8NYeE6IoFf34plbwK6O-l6ipWPKtB6mbdKZ68Bv-5-kpW-StN7SImj8_mPYXf8mdRJl_EIaGM-mCbMLrmKAJ0OzW/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2F5b2abcc5b65f7bca3e96f7c2e05d0da5531b5e03%2Fmris_compute_lgi%2Fmris_compute_lgi*L56__;Iw!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaO-Pl2JeA$

The `getmatlab` script:

https://secure-web.cisco.com/16T6BUAY9wNrUH8blOwHol6MvWiUMw-NBlGn_oAGvhHg-MQ...https://secure-web.cisco.com/1rcaQmk8gEY4TRxns_kq3Y-vfJQu9k_0f05Czu4vHvByy2yxZzk8DShzGVaAKQDyt2tberaj6r2-yrTlVt4E8r9UpGDiu_hdvy0ebq4lvxYEysJInVOtFhJ9nv4ZONUNfWvK0-2ct3x1CQTd2eo-sNwB17lHgr4woZFxtOW_cBvFDF3_vi8omF-30yzHg30Esm7VHGmdceoBuyHTdm3YBj7JZSCph3184WgpEizNrLPWVzJDcAd1gxa5Eb61n9ocGi_XieKnAjHWr1MMx1MTsQG3uQKVtH-AwkFgHFBTSMw_rtmtkHgipMdrHMhsUu4-H/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Ffsfast%2Fbin%2Fgetmatlab__;!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMQkTmFpg$

-Paul

________________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Na, Xiaoxu <XNA@uams.edumailto:XNA@uams.edu>

Sent: Thursday, December 7, 2023 12:03 PM

To: Freesurfer support list

Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

External Email - Use Caution

Thank you Paul! But I have already updated my neurodocker to the latest. I’ve tried to create a link using the same way you’ve listed below, and it didn’t help. In this way, I feel the mcr was not fully installed as I couldn’t locate the file MCRv97/bin/glnxa64/libmwlaunchermain.so, that’s why I turned to the official way, which installed a lot more files in that directory, but still not working.

The official way that R suggested, I feel like the script fs_install_mcr has already remove the temp it created during the installation once exit, so appending that to $LD_LIBRARY_PATH didn’t help. Any other tricks? Thanks so much!

Regards,

Xiaoxu

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Wighton, Paul

Sent: Thursday, December 7, 2023 10:35 AM

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>

Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

Hi Xiaoxu, This is how I built a FreeSurfer 7. 1. 1 container with matlabmcr 2014b (https: //urldefense. com/v3/__https: //github. com/pwighton/fs-docker/blob/master/notes/20201127-fs711-neurodocker-min. md*freesurfer711__;Iw!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g$)

ZjQcmQRYFpfptBannerStart

This Message Is From an External Sender

This message came from outside your organization.

ZjQcmQRYFpfptBannerEnd

Hi Xiaoxu,

This is how I built a FreeSurfer 7.1.1 container with matlabmcr 2014b

(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/17lmg4AkD6AmIjKkDyCPFjcxBYxH5098D0smecjLDjnTsPO...<https://secure-web.cisco.com/1NqpThoif7ehSo05oq6OO2t4FRTANtud3BsTPaBQYxBr_gT...https://secure-web.cisco.com/1T8X-kwEG5jikeZGlvstwnBZS-PllWyfX2gyveSn-XAY2KKLNRxyXuURZe9HNz_mc-2xVlyRqO4BxhC7BN6JGHeOxA3UHCvklGdMZ0hE4ID911JM0fHYOsL_BC1v_3G980YGWIpAJTNLCIO6-lI2YOlWWYnS_SsO2SUWgar66YYlx6g9ffN5NBeYs6PNw8L_LgS1fiK8cR8eCZpRhsmnU-juzaQ21d2B-yBIajsZPtYOO4P6B1m0q2TuXBo3fCj2S9yThgTnDSxz5P1Mb79KHGKpxOvbb_DYSg21PYir3ZUaL_xnpn5zNobWp7MKhb-aP/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fgithub.com%2Fpwighton%2Ffs-docker%2Fblob%2Fmaster%2Fnotes%2F20201127-fs711-neurodocker-min.md*freesurfer711__;Iw!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1KnnY8C5yTwrcARPclPPQqXaaF2UoxOeMqo5RQ4nwHj-68EbpR9U7X4dt88a3AFmGhyRRXTNll8XcHMzmIyiGyG-ndBLJzVgG2u56B2XGnM6nSQ0xLfeA2M8TeEz9oV8rEyDFKOur8CdGoNC6LLNYh9A8EJCV94l11edqMjtUkD35prfRNdeFFMPSgOEpvHyZHEaB7Hb9gntithqZrd0RaI6-CXM42edJaEuft1MqzhpKt6QlAm7yfDFmgBkFs2pyYkEVgPjYBKdPS4nafzy0nboAHyzt0PekaKfI8hWBZbI43Ray_nllXVobBZ4xc9lAMlZMylvy_66zSwcvv8-KbA/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fgithub.com*2Fpwighton*2Ffs-docker*2Fblob*2Fmaster*2Fnotes*2F20201127-fs711-neurodocker-min.md*2Afreesurfer711__*3BIw*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g*24__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaOmqycPgw$>)

```

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-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Na, Xiaoxu <XNA@uams.edu<mailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto:XNA@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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Cd7Deqzo-Wr-MuIdNthgdCdZOYhD0QmnFomVO2Rlr0eWvx...<https://secure-web.cisco.com/13xYUTBiXH-vkoimHRcmbgiWKfHiElsS_iA5edguzD_I8wW...https://secure-web.cisco.com/17XWjpMsM1TEXycG5V9e5DfwUQpW5Ma7GtopEh3WZDbJXTC5pgpfIG-3X8SCmC9xg4an5yKmWSHf5BpJEjQ9Bu8UNKWH0UajjvYm6NQpeD5QoI94O4KdHPJXR8Q1Hpx2Y0_LC4XEhf9crO784Zx0hYBrJCTdi2544fTSwrmpFmIewS6IN-oC__xfoOsbG3QDQaHETdt6E7biXE6Gauh8Bt6FAvyn6MEh8sb3d4w9Mu2_qhPpfm9fNXyBho6Ref30eVel3-2rL9PLI26SRU-eJ2_SMAOuW4lvlUOnUd8pXMlCLVbyqksHUiylp57Pf9bKy/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting__;!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1OaUQzJNRPo049e0G3gE7Svl2Z8-MWvMQ6O-8qzfk_20N7GLezlIKD7mW0K1Ee7_c_6_2zewxx7Iib8Knm_tTL-cwpOHfT5qvJpf6mdcuxX03P9uRuE0s-bZ3b3fBVSVbsf6nqSmmLShMDwtuliQ3EwTiON8GQMaC0ZKvHvkTjFXe4IFB_-2pMbktHuXm1MQQzrjpyu57CSZ_5u9tF8A9NRO47FkqmqYqwZo-DOyb0w5MeElRYx2c6By4DouUz8gziaDzP-eD4PbkttUmev26M3JGIRa1iTd82WeCZHoUh5z3TyDK0EkffTZjxw4YHz84OSP-IHY0DMYXF7QxBb49qw/https*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FBugReporting__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA*24__;JSUlJSUlJSUlJSUlJSU!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaN-J8pIDQ$><MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1YrL98qes1ttl9OHa3GEPNQfbqFRVvQUlCvHo1X_GYt7t3f...<https://secure-web.cisco.com/1ymCN-3y6iWCLLuhpKAyUsvFUYN0S_vKRDfm53JW03lTncK...https://secure-web.cisco.com/1ysFVW_r4ym7HkO-GNAc1WRViCZp2AuPkM1hj1H4ESv9QDDLvdS7qKdIzZ41dAmpm9d-ek-oHx2vLez8UukcCQ3mM72IghynXLXvFOtGnnLGNWJf6MyW1QvvJp2pbAyF3s98fAXgQVQPBnsMvpxXwQTluTAIDRRDQZwrYjPzYsi9C0H1P5CDk5rUnSE195_tY1JaDkOQKzjPzULvQGaEfPG7BCDOCG90wC6_7-Rp1-R8WUeRVXdDVk0bA6kpK4P3RrC4Xqhz7s-OVwp9uY-tAnFhNngE5TJwaslB2UHU86iP8BEry6aptKgld837LIGKX/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsecure-web.cisco.com%2F19z1ocn0OehHUGM4w6oiRnM6yr0UPgIGAZZxoya2UA2h4t8qi3-4qexKM59ajGsfrz7ib2U-SrmLHQdZJ95lZCAh6je5ny8UGsLOCbTJfwlv4NNCaud1J9PTBFJIAf6fW-q6Qgg-yyITcS1to7QYk6f6PkiT03tcV2wNsk_BYRJNamVMXwWfk427kOpr4mvddtzytLtss89btV4-SAEEA4n8ZVZadouTkCPGoFwXBjaixaBlKWkEl8J5An4a_s_aT5o73DUu8To4q274fToRd8hdlWU06g8RtrlKPoRn9-6ywNGQ0STILlB1T3OybZClLJ8DmyLCc4Z_ri49pguBC_g%2Fhttp*3A*2F*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FBugReporting__;JSUlJSU!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNRBpyMWeg$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/154gDIBAshQ8HHR1RYnGl5oJOAGCKfy7Le2H2zdSpvRu_hXHG3o05LsYwk6h3oBkC3AZwf9GFRNrZtpuMnrhjIwxoW55IyLyEN_r4a6Xm-7FT42hDcAZbXBDP7GOBqHwBJ4YUYq4ajs8LB3RDaaqGbRnUTd_7zMmBh3o-ITtXha0hrVIdLy9zh5OiHfQKpTu7EiMr_fsicwqoYygcBjRlcWN2yUm8E2QvD77mzLIhIBmucDTfB4wb9kHrz9Ic3QekuDYV5PxIOiCfgwhKVEXmSqN0cEIXv0EguMS624fQOyM2yD9F5LW9oJmzAGf0edOyEZktNCzl-KsEpDP2kH8ElQ/https*3A*2F*2Furldefense.com*2Fv3*2F____;JSUlJSU!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaO_xVIShg$

http%3A%2Fsecure-web.cisco.com%2F19z1ocn0OehHUGM4w6oiRnM6yr0UPgIGAZZxoya2UA2h4t8qi3-4qexKM59ajGsfrz7ib2U-SrmLHQdZJ95lZCAh6je5ny8UGsLOCbTJfwlv4NNCaud1J9PTBFJIAf6fW-q6Qgg-yyITcS1to7QYk6f6PkiT03tcV2wNsk_BYRJNamVMXwWfk427kOpr4mvddtzytLtss89btV4-SAEEA4n8ZVZadouTkCPGoFwXBjaixaBlKWkEl8J5An4a_s_aT5o73DUu8To4q274fToRd8hdlWU06g8RtrlKPoRn9-6ywNGQ0STILlB1T3OybZClLJ8DmyLCc4Z_ri49pguBC_g%2Fhttp%2A3A%2A2F%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2FBugReporting__%3BJSUlJSU%21%21LFqOYw%21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNRBpyMWeg%24>>

finish

From: fsbuild <fsbuild@contbay.com<mailto:fsbuild@contbay.com<mailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.commailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com>>>

Sent: Wednesday, December 6, 2023 9:14 PM

To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu>>

Cc: Na, Xiaoxu <XNA@uams.edu<mailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@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).

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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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/168ed9wFXDYoij4z9hx-4k14LEtisF2T3KlCFkdOK4hhay_...<https://secure-web.cisco.com/1lNapt2oDI65oxL0G2WK8V4wzngBbvg0fVS7Ej4TaWCOK_D...https://secure-web.cisco.com/1YmUf7IAjUciNco5ae5QtFuS8dKl9hdGFK2HPJf8SjI3p3HrjmMcPi0pW1blQDudGm7fLOhCVCppQ3rRmNIhmsF4rmiVcQS7xCmfaXQcwAvn0zfstdz_sX_Y79xhAWEW25dQqRHe0fj-4sNOsnUld1gnQVScRRcN5NzCvTltNXS92xoTZPGKnlomNDXM3cnplFQIb8JQ_b40s5bsNQgCUAOLtSOg7hnYvFYWzGWJHh1omeFS4W6OjptOorjzzQKnfoiFYb2a05gkUVgvF9INs0rzVcAe4ayHTaqqUJVEK6nj4N1G2As7LcCZ-cmWfOkdQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads__;!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQK2zaIeA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1J2CTZgiRcJrmtg5-7SfglDGEjwy8yt7335FB1LJGFTRe_drJNuSccrm-Yw9q3TwPPk9nBbsxMTVuDEMe64WpPbafz_pTt8BA7gBz-OPH6GQApL1oIpDgYevwzGQITPfJ1CQ235F2x69va42WvhKnwIOr2J2VN9JnFRYBEzr3znk8Equed0wTIzGU-mERXdKoFGTBTNTcSCy_OWv6B4TX914xTQh2Opm5nQB18d4Seu7hH8fUGxfhYEsWvphUvYYTrw7s42TcYU0qwM9XwbSmi8WDFUktpTM4xIhxgWzRiJEOQncbcltVQAxdVCKDqQo55NGAsxbsImeOdMDpsf8Tvg/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2Frel7downloads__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQK2zaIeA*24__;JSUlJSUlJSUlJSUlJSU!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMrCbA6nA$><MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ggeOmAsc1UAxv-IVVkMqWPzyRWkEiFY3JZMLxb3826wzFE...https://secure-web.cisco.com/1NfK1I76x5krVcan9hQeq7cBMosr3i2m41ZWRxyh8BvFQMBJLHEL0Lp_UcZ5NozP4gW1x55VoxZkIvfsq3cWIVDDNOdK6uB3oq3jA25ZzoGUn57LwBGuHbfCHEWti3T8keOKJ0ujiGaXVh_nq7JlJUbRk1k_r5OryWtPZDria08TwCK49p2Umk1dwUIN6x6J1s22Xzw6vVPUMQFJHLP4JNKZCAvBB2pR-z7iim-XAKzj_TlNAN0IFZ8kcRw5r67vVCWh9_yDJIea0ye50grJJnxgWjqPXXM_8R8y5CuMo1bViioqDLQJVLarQ6kmH5h3Q/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1M-gFnrnIJ-MOUpvREJw-JKitdgCKNA8aJw4B8Vg7lSCrwCLGKEux7EtwgiJMp3QQtgfuvSlzRJnFoOZo2PHM6a5WQzzITo6Vria4FgoDzsVgWzSwo-AxFOErH4zcGZ2_TNatyiGM7Mz_9wlFpbwIU7iK0g3_m5SXIPireLMIyiIC6r_20LFeiLyHMIha1AlqkevZZbMf7vXhTSqu_8KzxtoIVo3hrPSZQKeZ6O2NaKoz9PgqeiLeSTU2fVx4uyGRn6nVL8rBRf2m22BiLQlcjGA7BWqrQuG0XVZRWRv6hKAVRM6lbSD1wEF_uSOTmgI17hQDQYuH4PGtjNrQtU8v6A%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2Frel7downloads__*3B*21*21LFqOYw*21tDBZFrn3IUiIYFmlM2uL6_tGbVoPuNqWs5ClV4bXYLiasR-ZsSbQP2scMUQqGzU2mRnDo0R9cUG3gw*24__;JSUlJSUlJSUlJSUlJSU!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNToeRruxw$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1xEJosRhummDbLS1r_nTuzuMlruPQXKi-ilO5XJ4VTA5YD8_Yu20ZaLqHjvWHSPMCsazkIrAR_C_mSO5cxia8K8ULO-LTzLj6EzckVuvFWKsItZcQgcEPiIwhU1x48KxxO9qJRdgp3wupB4MNrMdyFgO6JhnV1EsgI9MeUi2Xvlp5F2_TFvbd6Ed5XOfldo5fYA5wOUc5tj08dZVVN2827FQKSDppTP7C4jPZ6WYM-F5KTACSWd0f4ZoyBiSlXmpGyXwWZKcqWh4-3r7_GR8HNL0kqg5kBM5tchuo98XLl91q6745p4IiRvIAeFnTqAb__kJvHoor1wPudIK_dhIQAg/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1M-gFnrnIJ-MOUpvREJw-JKitdgCKNA8aJw4B8Vg7lSCrwCLGKEux7EtwgiJMp3QQtgfuvSlzRJnFoOZo2PHM6a5WQzzITo6Vria4FgoDzsVgWzSwo-AxFOErH4zcGZ2_TNatyiGM7Mz_9wlFpbwIU7iK0g3_m5SXIPireLMIyiIC6r_20LFeiLyHMIha1AlqkevZZbMf7vXhTSqu_8KzxtoIVo3hrPSZQKeZ6O2NaKoz9PgqeiLeSTU2fVx4uyGRn6nVL8rBRf2m22BiLQlcjGA7BWqrQuG0XVZRWRv6hKAVRM6lbSD1wEF_uSOTmgI17hQDQYuH4PGtjNrQtU8v6A*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2Fsurfer.nmr.mgh.harvard.edu*2A2Ffswiki*2A2Frel7downloads__*2A3B*2A21*2A21LFqOYw*2A21tDBZFrn3IUiIYFmlM2uL6_tGbVoPuNqWs5ClV4bXYLiasR-ZsSbQP2scMUQqGzU2mRnDo0R9cUG3gw*2A24__*3BJSUlJSUlJSUlJSUlJSU*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNToeRruxw*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaP5BfrC4Q$

qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNToeRruxw$<https://secure-web.cisco.com/148hI1t4UV-NJWSybLYC7HRTnsxfdtJOhQrxz_vyBFCI_Ln...https://secure-web.cisco.com/1NfK1I76x5krVcan9hQeq7cBMosr3i2m41ZWRxyh8BvFQMBJLHEL0Lp_UcZ5NozP4gW1x55VoxZkIvfsq3cWIVDDNOdK6uB3oq3jA25ZzoGUn57LwBGuHbfCHEWti3T8keOKJ0ujiGaXVh_nq7JlJUbRk1k_r5OryWtPZDria08TwCK49p2Umk1dwUIN6x6J1s22Xzw6vVPUMQFJHLP4JNKZCAvBB2pR-z7iim-XAKzj_TlNAN0IFZ8kcRw5r67vVCWh9_yDJIea0ye50grJJnxgWjqPXXM_8R8y5CuMo1bViioqDLQJVLarQ6kmH5h3Q/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1M-gFnrnIJ-MOUpvREJw-JKitdgCKNA8aJw4B8Vg7lSCrwCLGKEux7EtwgiJMp3QQtgfuvSlzRJnFoOZo2PHM6a5WQzzITo6Vria4FgoDzsVgWzSwo-AxFOErH4zcGZ2_TNatyiGM7Mz_9wlFpbwIU7iK0g3_m5SXIPireLMIyiIC6r_20LFeiLyHMIha1AlqkevZZbMf7vXhTSqu_8KzxtoIVo3hrPSZQKeZ6O2NaKoz9PgqeiLeSTU2fVx4uyGRn6nVL8rBRf2m22BiLQlcjGA7BWqrQuG0XVZRWRv6hKAVRM6lbSD1wEF_uSOTmgI17hQDQYuH4PGtjNrQtU8v6A%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2Frel7downloads__*3B*21*21LFqOYw*21tDBZFrn3IUiIYFmlM2uL6_tGbVoPuNqWs5ClV4bXYLiasR-ZsSbQP2scMUQqGzU2mRnDo0R9cUG3gw*24__;JSUlJSUlJSUlJSUlJSU!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNToeRruxw$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1xEJosRhummDbLS1r_nTuzuMlruPQXKi-ilO5XJ4VTA5YD8_Yu20ZaLqHjvWHSPMCsazkIrAR_C_mSO5cxia8K8ULO-LTzLj6EzckVuvFWKsItZcQgcEPiIwhU1x48KxxO9qJRdgp3wupB4MNrMdyFgO6JhnV1EsgI9MeUi2Xvlp5F2_TFvbd6Ed5XOfldo5fYA5wOUc5tj08dZVVN2827FQKSDppTP7C4jPZ6WYM-F5KTACSWd0f4ZoyBiSlXmpGyXwWZKcqWh4-3r7_GR8HNL0kqg5kBM5tchuo98XLl91q6745p4IiRvIAeFnTqAb__kJvHoor1wPudIK_dhIQAg/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1M-gFnrnIJ-MOUpvREJw-JKitdgCKNA8aJw4B8Vg7lSCrwCLGKEux7EtwgiJMp3QQtgfuvSlzRJnFoOZo2PHM6a5WQzzITo6Vria4FgoDzsVgWzSwo-AxFOErH4zcGZ2_TNatyiGM7Mz_9wlFpbwIU7iK0g3_m5SXIPireLMIyiIC6r_20LFeiLyHMIha1AlqkevZZbMf7vXhTSqu_8KzxtoIVo3hrPSZQKeZ6O2NaKoz9PgqeiLeSTU2fVx4uyGRn6nVL8rBRf2m22BiLQlcjGA7BWqrQuG0XVZRWRv6hKAVRM6lbSD1wEF_uSOTmgI17hQDQYuH4PGtjNrQtU8v6A*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2Fsurfer.nmr.mgh.harvard.edu*2A2Ffswiki*2A2Frel7downloads__*2A3B*2A21*2A21LFqOYw*2A21tDBZFrn3IUiIYFmlM2uL6_tGbVoPuNqWs5ClV4bXYLiasR-ZsSbQP2scMUQqGzU2mRnDo0R9cUG3gw*2A24__*3BJSUlJSUlJSUlJSUlJSU*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNToeRruxw*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaP5BfrC4Q$>>.

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<mailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto: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

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Regards,

Xiaoxu

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Thank you so much for your confirmation, Paul! Then I guess I need to shove them back to my work station to continue if I couldn’t put a full matlab into the container. Thank you for saving me the time trying the mcr!

Regards, Xiaoxu

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Wighton, Paul Sent: Thursday, December 7, 2023 12:09 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

It looks like mris_compute_lgi won't work with *any* mcr and needs a full matlab installation. Sorry :( -Paul ________________________________________ From: freesurfer-bounces@ nmr. mgh. harvard. edu <freesurfer-bounces@ nmr. mgh. harvard. edu> ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd

It looks like mris_compute_lgi won't work with *any* mcr and needs a full matlab installation.

Sorry :(

-Paul

________________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Na, Xiaoxu <XNA@uams.edumailto:XNA@uams.edu>

Sent: Thursday, December 7, 2023 1:00 PM

To: Freesurfer support list

Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

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Hi Paul,

Thank you so much for your confirmation! This is exactly what I’m having trouble with. In this case, maybe I can’t go with 7.3.1 and upper, I can go back to work with 7.1.1. Have you tried with 7.1.1 with mcrv84(matlab 2014b) running correctly? Last time I run LGI was on my own workstation with 7.1.0 and full matlab 2018b installed. Since I want to run all subjects on HPC this time, I have to build a docker to support that. If you have any version of freesurfer-mcr pair that is working for LGI, will you please kindly let me know and I’ll give it a try too? Thank you so much!

Regards,

Xiaoxu

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Wighton, Paul

Sent: Thursday, December 7, 2023 11:54 AM

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>

Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

I just tried this in a container. It looks like `mris_compute_lgi` is not designed to work with the mcr, and needs a full matlab installation. I started by jumping into a freesurfer 7. 3. 1 container. ``` docker run -it --rm freesurfer/freesurfer: 7. 3. 2

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I just tried this in a container. It looks like `mris_compute_lgi` is not designed to work with the mcr, and needs a full matlab installation.

I started by jumping into a freesurfer 7.3.1 container.

```

docker run -it --rm freesurfer/freesurfer:7.3.2

```

Then I installed matlab mcr

```

fs_install_mcr R2019b

```

Note the output `fs_install_mcr` says:

```

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

/tmp/tmp.AzujBUG5W7/install-target/v97/runtime/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/bin/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/sys/os/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/extern/bin/glnxa64

```

But this is what should be added to the `LD_LIBRARY_PATH`:

```

export LD_LIBRARY_PATH=${FREESURFER_HOME}/MCRv97/runtime/glnxa64:${FREESURFER_HOME}/MCRv97/bin/glnxa64:${FREESURFER_HOME}/MCRv97/sys/os/glnxa64:${FREESURFER_HOME}/MCRv97/extern/bin/glnxa64:${LD_LIBRARY_PATH}

```

And I can confirm the `mris_compute_lgi` indeed does not work:

```

mris_compute_lgi --i $FREESURFER_HOME/subjects/bert/surf/lh.pial

ERROR: Matlab is required to run mris_compute_lgi!

```

But it looks like the mcr was installed:

```

find $FREESURFER_HOME/MCRv97

```

The error is a result of `getmatlab` not being able to find the matlab binary, which isn't included in the MCR.

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The `getmatlab` script:

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-Paul

________________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Na, Xiaoxu <XNA@uams.edu<mailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto:XNA@uams.edu>>

Sent: Thursday, December 7, 2023 12:03 PM

To: Freesurfer support list

Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

External Email - Use Caution

Thank you Paul! But I have already updated my neurodocker to the latest. I’ve tried to create a link using the same way you’ve listed below, and it didn’t help. In this way, I feel the mcr was not fully installed as I couldn’t locate the file MCRv97/bin/glnxa64/libmwlaunchermain.so, that’s why I turned to the official way, which installed a lot more files in that directory, but still not working.

The official way that R suggested, I feel like the script fs_install_mcr has already remove the temp it created during the installation once exit, so appending that to $LD_LIBRARY_PATH didn’t help. Any other tricks? Thanks so much!

Regards,

Xiaoxu

From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Wighton, Paul

Sent: Thursday, December 7, 2023 10:35 AM

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu>>

Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

Hi Xiaoxu, This is how I built a FreeSurfer 7. 1. 1 container with matlabmcr 2014b (https: //urldefense. com/v3/__https: //github. com/pwighton/fs-docker/blob/master/notes/20201127-fs711-neurodocker-min. md*freesurfer711__;Iw!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g$)

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Hi Xiaoxu,

This is how I built a FreeSurfer 7.1.1 container with matlabmcr 2014b

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CdGoNC6LLNYh9A8EJCV94l11edqMjtUkD35prfRNdeFFMPSgOEpvHyZHEaB7Hb9gntithqZrd0RaI6-CXM42edJaEuft1MqzhpKt6QlAm7yfDFmgBkFs2pyYkEVgPjYBKdPS4nafzy0nboAHyzt0PekaKfI8hWBZbI43Ray_nllXVobBZ4xc9lAMlZMylvy_66zSwcvv8-KbA%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fgithub.com%2A2Fpwighton%2A2Ffs-docker%2A2Fblob%2A2Fmaster%2A2Fnotes%2A2F20201127-fs711-neurodocker-min.md%2A2Afreesurfer711__%2A3BIw%2A21%2A21LFqOYw%2A21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJQ%21%21LFqOYw%21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaOmqycPgw%24>>)

```

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-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>>> on behalf of Na, Xiaoxu <XNA@uams.edu<mailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/131oSWsf-uspjx7ZY2E-k8LFQYHctyrEltb2qkGeXGjUCGG...<https://secure-web.cisco.com/1FSSkWEGTIngqO-ADxLjSlKPtCbdh-AsD8eEr42c-pBNDTL...<https://secure-web.cisco.com/145tJ7FqF9oN-AutSpMYcE0LBX0G7U_ZiHlQbN2fwriUc1x...https://secure-web.cisco.com/1SCzPvPWXqdLBaLPWEqGcC3tdXhv0Wl10Wwh-Vpg0WqMeiM4LIbDvq3pG9Jgw2X90RdWPY806DwJNMMJp5vdJX56HPI09xGHMagENBVGh4uzG34eqlBrYU0b-BZGmKA_7I4LY4CjX0fJPHX0LHRVWBDNYIEPihjXKlfFClDWAmNNfqVS_Q5zPnGmG7MCn-5OGmsYEvIXmwX3eAzbm94cshFXP0rL52o4wSexFvXrLc1x3hoJr0jfkl7KUe6mBDuKpVM_OMBPyYTrcQcLSELEnzqstDdMqp6qE6d-E8swsm9fIIPL7pG2kf7YJHC4ZaGxA/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting__;!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1OaUQzJNRPo049e0G3gE7Svl2Z8-MWvMQ6O-8qzfk_20N7GLezlIKD7mW0K1Ee7_c_6_2zewxx7Iib8Knm_tTL-cwpOHfT5qvJpf6mdcuxX03P9uRuE0s-bZ3b3fBVSVbsf6nqSmmLShMDwtuliQ3EwTiON8GQMaC0ZKvHvkTjFXe4IFB_-2pMbktHuXm1MQQzrjpyu57CSZ_5u9tF8A9NRO47FkqmqYqwZo-DOyb0w5MeElRYx2c6By4DouUz8gziaDzP-eD4PbkttUmev26M3JGIRa1iTd82WeCZHoUh5z3TyDK0EkffTZjxw4YHz84OSP-IHY0DMYXF7QxBb49qw/https*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FBugReporting__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA*24__;JSUlJSUlJSUlJSUlJSU!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaN-J8pIDQ$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1XQCbKYk8dPlPndcc-CWngT1LMlXOkav_qc5WZkzwS1_W8nGf1ewc1odzRecVmXVbCdTtHWBWPEhTynwSihjw9zIm9vI7_ok39sPyY25kL8ZcrKLGKefqQhcFcZ7jRb6UHQ58824zswlD6khQ-wIoBG_s8Vn1tNNlWg1D8tu81SiOGE9ehQuikt3h74iAKqnusd1GyLWfrlkvVo2Qrut1qCWDPfvIIVv4-Dx2fx78k3rSdqeE2wG-M-9Z5Hh7cCx0b0FEyD4JPcRtY_pnDB-KJFJ6_TGMlKBxOUSHXQRkfUt1JjL-YhvfIKrL5VlxvDdL/https*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FBugReporting__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA*24*253chttps*3A*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1OaUQzJNRPo049e0G3gE7Svl2Z8-MWvMQ6O-8qzfk_20N7GLezlIKD7mW0K1Ee7_c_6_2zewxx7Iib8Knm_tTL-cwpOHfT5qvJpf6mdcuxX03P9uRuE0s-bZ3b3fBVSVbsf6nqSmmLShMDwtuliQ3EwTiON8GQMaC0ZKvHvkTjFXe4IFB_-2pMbktHuXm1MQQzrjpyu57CSZ__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMp1xOZ-wQ$

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finish

From: fsbuild <fsbuild@contbay.com<mailto:fsbuild@contbay.com<mailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com<mailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.commailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com>>>>

Sent: Wednesday, December 6, 2023 9:14 PM

To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu>>>

Cc: Na, Xiaoxu <XNA@uams.edu<mailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@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).

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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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZAiKXnN8LTZFBXdRJm133cqmJUzdlUYVvICC68OPIIOm1M...<https://secure-web.cisco.com/1UnQ31EeDPd6tFd3Yxznjx4e7Dw-3M12DbxeAl-v_XFqhSA...<https://secure-web.cisco.com/1azXcpruebzOdsKp7RTgXmlWK3PK4RPJz_LkQueY_cb4W2i...https://secure-web.cisco.com/1Q0petjaDpOg4nkHuKCoYAnIb8svtpF-EmQwSbw9ZJHGy2gPgzjY66SSAy5NzYXMh2OUgwDyYOtIop15u8XSU964PwuXwW_cVF1mnljRS6mXeb8G774PEq32VNiYFZXH3YcKSVJDUpt3vYJYQ9ZFTv1zwX1WuLrDQ2YCiu14b3Yz-YbmdYwe6C_V-XgGCzXeBZWTpzUAX0gC-yYCvIt_kOeq24Vs7VKliKvEAucjyP4mUN10Rl2DFe3w4M4ooQm_znyCdswcHr0w21llZW7zyMu5RMXrKPoXOF94HC56FJOHCedoNtgJQYmhkVofK4Udl/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads__;!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQK2zaIeA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1J2CTZgiRcJrmtg5-7SfglDGEjwy8yt7335FB1LJGFTRe_drJNuSccrm-Yw9q3TwPPk9nBbsxMTVuDEMe64WpPbafz_pTt8BA7gBz-OPH6GQApL1oIpDgYevwzGQITPfJ1CQ235F2x69va42WvhKnwIOr2J2VN9JnFRYBEzr3znk8Equed0wTIzGU-mERXdKoFGTBTNTcSCy_OWv6B4TX914xTQh2Opm5nQB18d4Seu7hH8fUGxfhYEsWvphUvYYTrw7s42TcYU0qwM9XwbSmi8WDFUktpTM4xIhxgWzRiJEOQncbcltVQAxdVCKDqQo55NGAsxbsImeOdMDpsf8Tvg/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2Frel7downloads__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQK2zaIeA*24__;JSUlJSUlJSUlJSUlJSU!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMrCbA6nA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1YcV6Y1tdz08V8rqoFceWLuOmHKpNTfhJbfW5LYtXrwCGjKsuOII75kS1Bf-doQC6sCoIIJjf6cNLO3HJ1pzrTmSa1yKdhB-n7k0YjxbqzflMRDAfIf8oG9n1tKWNBBimHR1OwepG63jv0UsHzT9e3MVJm5onsFbzL_OMairlifJwedhw3Z9w3rxu8affDgHdjx_iLdhsUGmvfHQzyfHypelsIjR53FeRe8unCW0cMucTwK60qQiQ0_ztOZCEcZUtWKTY5MetrcszeyuKD3OrtJljxPLx0WTp60_9P5NfX8ZmH9z-UbvXBvsW1SvgXHIM/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2Frel7downloads__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMd__;JSUlJSUlJSUlJSUlJQ!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMrJ96KQWw$

Q_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQK2zaIeA%24%253chttps%3A%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1J2CTZgiRcJrmtg5-7SfglDGEjwy8yt7335FB1LJGFTRe_drJNuSccrm-Yw9q3TwPPk9nBbsxMTVuDEMe64WpPbafz_pTt8BA7gBz-OPH6GQApL1oIpDgYevwzGQITPfJ1CQ235F2x69va42WvhKnwIOr2J2VN9JnFRYBEzr3znk8Equed0wTIzGU-mERXdKoFGTBTNTcSCy_OWv6B4TX914xTQh2Opm5nQB18d4Seu7hH8fUGxfhYEsWvphUvYYTrw7s42TcYU0qwM9XwbSmi8WDFUktpTM4xIhxgWzRiJEOQncbcltVQAxdVCKDqQo55NGAsxbsImeOdMDpsf8Tvg%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2Frel7downloads__%2A3B%2A21%2A21LFqOYw%2A21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQK2zaIeA%2A24__%3BJSUlJSUlJSUlJSUlJSU%21%21LFqOYw%21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMrCbA6nA%24>><MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1PLq9gjxn7QDZe4HsAdnDcI0yM2byYRlUbY9od9VtpUpn2Y...<https://secure-web.cisco.com/1AZTDwY4dGM8rYt-XZ-rfg-JDZZ_trjv7MJYKRlyK8IWaje...https://secure-web.cisco.com/1WTMbYX-3bLZK6b9DybYHMHqQcMSRCv3Xhs953VwcGa1okivnTVXmSqlGbg8SEmixklnAHRRO5uiEFpg5sPVObTHUlFmxH1HTr9V6xZ8j_Me7I2wDQmmuERgaAcJPh7jCQZfirzfZFlbgq3X1Jh__hj-LAnLZmbkwh6VxqEUSwDal-_pqQVrcmDGAHngYsxU8VQKH3bhDaLOfeOhGg2s3kUM8sJlzHy47bv9fNFeBDMT5u6sh6qEGUGDUsurP7HmSj2vyxs8Rr8jMFuZxOH7BbUlTnvpTBNM-_5IySzgdDAvLNq9Lgu4Uy4fp7MFTGcgI/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1M-gFnrnIJ-MOUpvREJw-JKitdgCKNA8aJw4B8Vg7lSCrwCLGKEux7EtwgiJMp3QQtgfuvSlzRJnFoOZo2PHM6a5WQzzITo6Vria4FgoDzsVgWzSwo-AxFOErH4zcGZ2_TNatyiGM7Mz_9wlFpbwIU7iK0g3_m5SXIPireLMIyiIC6r_20LFeiLyHMIha1AlqkevZZbMf7vXhTSqu_8KzxtoIVo3hrPSZQKeZ6O2NaKoz9PgqeiLeSTU2fVx4uyGRn6nVL8rBRf2m22BiLQlcjGA7BWqrQuG0XVZRWRv6hKAVRM6lbSD1wEF_uSOTmgI17hQDQYuH4PGtjNrQtU8v6A%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2Frel7downloads__*3B*21*21LFqOYw*21tDBZFrn3IUiIYFmlM2uL6_tGbVoPuNqWs5ClV4bXYLiasR-ZsSbQP2scMUQqGzU2mRnDo0R9cUG3gw*24__;JSUlJSUlJSUlJSUlJSU!!LFqOYw!rrxnktSjJS824%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1LjrkozsstV5E7J8cYzL3jBK3N0aeqGGCCzcXLVS8VGpKtd1mOvQwaJHwCppiVWsAru1nCTWqtBiogNF0Qyn6rBHT5ckFU8oVfJR9Motp96I-YnlrDA-L7sLDsNLMm5FNJ3qf5mqKclVmM9Pu_vI_9prIe0mn7bya_U3n2i9mz3eSHGTMSMq3QLVDu1impaeTFDmmqeOzVKZLjGr26zapRhg9F3QlaXLuJ7TQaWmqFR-FqYqaoxL5UqI9f8WLfdMiyQk49EIuU7_gtzNVkbUfLw/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web__;JSUlJSUlJQ!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMp6HHuvYQ$

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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNToeRruxw$<https://secure-web.cisco.com/1IO2-YHo9wayyGd_yt7RoHqN3hEkKnj0KUFst7oVcCMZhp_...<https://secure-web.cisco.com/1AZTDwY4dGM8rYt-XZ-rfg-JDZZ_trjv7MJYKRlyK8IWaje...https://secure-web.cisco.com/1ScL4zFBZz6-r5fJCDdKHnQWJfa7S_E70qIVnKgmSNfoKpBmcpoEe5eh3JSJF7uo91zRdAh-ozN32yw9-QXPs5PLaqlVbSxoh9Ik_HMik7wO9mGeR1EWdEV0VujqQOCqiPQosBjS16joJT9H2uQ2016hsTkVgo7URNYXGjKlR3oiBaRJBd3NjVDfmamId-UDYr5559YnA8_ac45feZVAxZMGpWoZdUDJTiENkp3SKfQA262-7d7Mos48r00urxSm97RifNmT4qWb_TRHD3oDIE4Pl6-shh6RIgUd9Uo2Fre5rvvVKkRPKJYDgtb0GIeib/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1xEJosRhummDbLS1r_nTuzuMlruPQXKi-ilO5XJ4VTA5YD8_Yu20ZaLqHjvWHSPMCsazkIrAR_C_mSO5cxia8K8ULO-LTzLj6EzckVuvFWKsItZcQgcEPiIwhU1x48KxxO9qJRdgp3wupB4MNrMdyFgO6JhnV1EsgI9MeUi2Xvlp5F2_TFvbd6Ed5XOfldo5fYA5wOUc5tj08dZVVN2827FQKSDppTP7C4jPZ6WYM-F5KTACSWd0f4ZoyBiSlXmpGyXwWZKcqWh4-3r7_GR8HNL0kqg5kBM5tchuo98XLl91q6745p4IiRvIAeFnTqAb__kJvHoor1wPudIK_dhIQAg%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1M-gFnrnIJ-MOUpvREJw-JKitdgCKNA8aJw4B8Vg7lSCrwCLGKEux7EtwgiJMp3QQtgfuvSlzRJnFoOZo2PHM6a5WQzzITo6Vria4FgoDzsVgWzSwo-AxFOErH4zcGZ2_TNatyiGM7Mz_9wlFpbwIU7iK0g3_m5SXIPireLMIyiIC6r_20LFeiLyHMIha1AlqkevZZbMf7vXhTSqu_8KzxtoIVo3hrPSZQKeZ6O2NaKoz9PgqeiLeSTU2fVx4uyGRn6nVL8rBRf2m22BiLQlcjGA7BWqrQuG0XVZRWRv6hKAVRM6lbSD1wEF_uSOTmgI17hQDQYuH4PGtjNrQtU8v6A*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__https*2A3A*2A2Fsurfer.nmr.mgh.harvard.edu*2A2Ffswiki*2A2Frel7downloads__*2A3B*2A21*2A21LFqOYw*2A21tDBZFrn3IUiIYFmlM2uL6_tGbVoPuNqWs5ClV4bXYLiasR-ZsSbQP2scMUQqGzU2mRnDo0R9cUG3gw*2A24__*3BJSUlJSUlJSUlJSUlJSU*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNToeRruxw*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaP5BfrC4Q$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1LjrkozsstV5E7J8cYzL3jBK3N0aeqGGCCzcXLVS8VGpKtd1mOvQwaJHwCppiVWsAru1nCTWqtBiogNF0Qyn6rBHT5ckFU8oVfJR9Motp96I-YnlrDA-L7sLDsNLMm5FNJ3qf5mqKclVmM9Pu_vI_9prIe0mn7bya_U3n2i9mz3eSHGTMSMq3QLVDu1impaeTFDmmqeOzVKZLjGr26zapRhg9F3QlaXLuJ7TQaWmqFR-FqYqaoxL5UqI9f8WLfdMiyQk49EIuU7_gtzNVkbUfLw/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1M-gFnrnIJ-MOUpvREJw-JKitdgCKNA8aJw4B8Vg7lSCrwCLGKEux7EtwgiJMp3QQtgfuvSlzRJnFoOZo2PHM6a5WQzzITo6Vria4FgoDzsVgWzSwo-AxFOErH4zcGZ2_TNatyiGM7Mz_9wlFpbwIU7iK0g3_m5SXIPireLMIyiIC6r_20LFeiLyH__;JSUlJSUlJSU!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMqDCDS3Hg$

MIha1AlqkevZZbMf7vXhTSqu_8KzxtoIVo3hrPSZQKeZ6O2NaKoz9PgqeiLeSTU2fVx4uyGRn6nVL8rBRf2m22BiLQlcjGA7BWqrQuG0XVZRWRv6hKAVRM6lbSD1wEF_uSOTmgI17hQDQYuH4PGtjNrQtU8v6A%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsurfer.nmr.mgh.harvard.edu%2A2Ffswiki%2A2Frel7downloads__%2A3B%2A21%2A21LFqOYw%2A21tDBZFrn3IUiIYFmlM2uL6_tGbVoPuNqWs5ClV4bXYLiasR-ZsSbQP2scMUQqGzU2mRnDo0R9cUG3gw%2A24__%3BJSUlJSUlJSUlJSUlJSU%21%21LFqOYw%21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNToeRruxw%24%253chttps%3A%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1xEJosRhummDbLS1r_nTuzuMlruPQXKi-ilO5XJ4VTA5YD8_Yu20ZaLqHjvWHSPMCsazkIrAR_C_mSO5cxia8K8ULO-LTzLj6EzckVuvFWKsItZcQgcEPiIwhU1x48KxxO9qJRdgp3wupB4MNrMdyFgO6JhnV1EsgI9MeUi2Xvlp5F2_TFvbd6Ed5XOfldo5fYA5wOUc5tj08dZVVN2827FQKSDppTP7C4jPZ6WYM-F5KTACSWd0f4ZoyBiSlXmpGyXwWZKcqWh4-3r7_GR8HNL0kqg5kBM5tchuo98XLl91q6745p4IiRvIAeFnTqAb__kJvHoor1wPudIK_dhIQAg%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F1M-gFnrnIJ-MOUpvREJw-JKitdgCKNA8aJw4B8Vg7lSCrwCLGKEux7EtwgiJMp3QQtgfuvSlzRJnFoOZo2PHM6a5WQzzITo6Vria4FgoDzsVgWzSwo-AxFOErH4zcGZ2_TNatyiGM7Mz_9wlFpbwIU7iK0g3_m5SXIPireLMIyiIC6r_20LFeiLyHMIha1AlqkevZZbMf7vXhTSqu_8KzxtoIVo3hrPSZQKeZ6O2NaKoz9PgqeiLeSTU2fVx4uyGRn6nVL8rBRf2m22BiLQlcjGA7BWqrQuG0XVZRWRv6hKAVRM6lbSD1wEF_uSOTmgI17hQDQYuH4PGtjNrQtU8v6A%2A2Fhttps%2A2A3A%2A2A2F%2A2A2Furldefense.com%2A2A2Fv3%2A2A2F__https%2A2A3A%2A2A2Fsurfer.nmr.mgh.harvard.edu%2A2A2Ffswiki%2A2A2Frel7downloads__%2A2A3B%2A2A21%2A2A21LFqOYw%2A2A21tDBZFrn3IUiIYFmlM2uL6_tGbVoPuNqWs5ClV4bXYLiasR-ZsSbQP2scMUQqGzU2mRnDo0R9cUG3gw%2A2A24__%2A3BJSUlJSUlJSUlJSUlJSU%2A21%2A21LFqOYw%2A21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNToeRruxw%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ%21%21LFqOYw%21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaP5BfrC4Q%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 (XNA@uams.edu<mailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto: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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/131oSWsf-uspjx7ZY2E-k8LFQYHctyrEltb2qkGeXGjUCGG...<https://secure-web.cisco.com/1FSSkWEGTIngqO-ADxLjSlKPtCbdh-AsD8eEr42c-pBNDTL...<https://secure-web.cisco.com/145tJ7FqF9oN-AutSpMYcE0LBX0G7U_ZiHlQbN2fwriUc1x...https://secure-web.cisco.com/1SCzPvPWXqdLBaLPWEqGcC3tdXhv0Wl10Wwh-Vpg0WqMeiM4LIbDvq3pG9Jgw2X90RdWPY806DwJNMMJp5vdJX56HPI09xGHMagENBVGh4uzG34eqlBrYU0b-BZGmKA_7I4LY4CjX0fJPHX0LHRVWBDNYIEPihjXKlfFClDWAmNNfqVS_Q5zPnGmG7MCn-5OGmsYEvIXmwX3eAzbm94cshFXP0rL52o4wSexFvXrLc1x3hoJr0jfkl7KUe6mBDuKpVM_OMBPyYTrcQcLSELEnzqstDdMqp6qE6d-E8swsm9fIIPL7pG2kf7YJHC4ZaGxA/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting__;!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1OaUQzJNRPo049e0G3gE7Svl2Z8-MWvMQ6O-8qzfk_20N7GLezlIKD7mW0K1Ee7_c_6_2zewxx7Iib8Knm_tTL-cwpOHfT5qvJpf6mdcuxX03P9uRuE0s-bZ3b3fBVSVbsf6nqSmmLShMDwtuliQ3EwTiON8GQMaC0ZKvHvkTjFXe4IFB_-2pMbktHuXm1MQQzrjpyu57CSZ_5u9tF8A9NRO47FkqmqYqwZo-DOyb0w5MeElRYx2c6By4DouUz8gziaDzP-eD4PbkttUmev26M3JGIRa1iTd82WeCZHoUh5z3TyDK0EkffTZjxw4YHz84OSP-IHY0DMYXF7QxBb49qw/https*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FBugReporting__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA*24__;JSUlJSUlJSUlJSUlJSU!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaN-J8pIDQ$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1XQCbKYk8dPlPndcc-CWngT1LMlXOkav_qc5WZkzwS1_W8nGf1ewc1odzRecVmXVbCdTtHWBWPEhTynwSihjw9zIm9vI7_ok39sPyY25kL8ZcrKLGKefqQhcFcZ7jRb6UHQ58824zswlD6khQ-wIoBG_s8Vn1tNNlWg1D8tu81SiOGE9ehQuikt3h74iAKqnusd1GyLWfrlkvVo2Qrut1qCWDPfvIIVv4-Dx2fx78k3rSdqeE2wG-M-9Z5Hh7cCx0b0FEyD4JPcRtY_pnDB-KJFJ6_TGMlKBxOUSHXQRkfUt1JjL-YhvfIKrL5VlxvDdL/https*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FBugReporting__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA*24*253chttps*3A*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1OaUQzJNRPo049e0G3gE7Svl2Z8-MWvMQ6O-8qzfk_20N7GLezlIKD7mW0K1Ee7_c_6_2zewxx7Iib8Knm_tTL-cwpOHfT5qvJpf6mdcuxX03P9uRuE0s-bZ3b3fBVSVbsf6nqSmmLShMDwtuliQ3EwTiON8GQMaC0ZKvHvkTjFXe4IFB_-2pMbktHuXm1MQQzrjpyu57CSZ__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMp1xOZ-wQ$

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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be SUlJSUlJSUlJSUlJSUlJSUlJQ!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQsIpGdmg$<https://secure-web.cisco.com/1h6I0hl3Cft_L5c79Qq2HpuXO6-GimRvKq1zhhOoERbXhbv...<https://secure-web.cisco.com/1e0Bl1mi88TFnYYp2MvCgcNSuDYAj9Iush7eBARUenwICPT...https://secure-web.cisco.com/1zrg9JJKS39cguhRbSv4vWi1NK9WHNH3es-ORYuirUitl95ZNHKWnj9b6V75s1jZ4O93n6IhwH15DaSLkoJ04P0ICWhAMwSfgpUqJ6S3lDeIk9I-jKDWqJ7UByCdgG-0eyzyZ1O7stiOGXTuSOpNaQK00kukVo2KNaSeD6H5NTWNmc76ciSkoYKG1RoBpE1z6vkY0Jv-INVY-KnZwsVD-1SCpo2oSGkkgcuxv8fV7kb5Ebg2IHmMKv8DGyBSPmY4ucERGQEdtJqYbTkqaVFjhkuaq_G5qfq-T3vn0r66Zc0ZLDsIrdsqvyeIrG22Pqms1/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1bxNhJu54ayIk66WfxscaLvkW-UFq2I7X32tTh8RP9yO9jaZpaLTZQU3ywzVsJi_J7nC_LKVuzqLM8_Ke2-ZbNm0S2tEZTGXLWg6rqUyq1bNTW7pXeUuv4OIMExHcC_4J8ZppcjpF-lElFzAEo2aDukFYcuBr5gThdr91LkHWsYBYKgzVWnDo1L518WiYopAVe7YjI_nJ962wavxwewHvdhAMsWEQzusmaNaWUTzP19blExB_GRCWkdaS2bvyU6nWX9NSdYogmKcqgYal7Re4UKOluJ7DnETJvEgxeNu_APRiNTtjZt4JlH8Kgg3D4Lh3O9Uv9qAUSjiGzwHw2Avtbw%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1hvYCCErje-MUOn9IgzcBShRONns5bVbUWgfe-ybvxkeCQa2gIQlOS_2ObCm5I_CEqVuEeu5EqMfmd2ItEpPJTOED7VMKPdA0H-auEU39CBYG_vsAkS0JPR1dM3AdH7iKUu9ncN7HDb-C_Yhd1U1phTFbp6VPbH1W9s9-DqLs9ZGPkS-S-0ZoIz3m4ic0fzlAelfRc2xzP8EwgcmvjYSWDi5D8XrNVJEjEZmQSgPW2prZhibd6zS6ZgXNT11sS5ldkYUB3ppsF3-oeAlvHQwnylP55vYsgL1tP2OKAKIuuMfz9PxQXlQPRYm5A34M-WKlB3yLxLo7EAxfeBq2RL9OKQ*2Fhttps*2A3A*2A2F*2A2Furldefense.com*2A2Fv3*2A2F__http*2A3A*2A2Fsecure-web.cisco.com*2A2F10JlU9uC5Jx9CmqgAZa_0KlYFqyorcNvk6q66KAYmJMeQk0FWzT50gXlpuJkzmflxujtyczft13iy1XlOsnHw9vCdbPpJzZrFOkTwiHQIKrSROUzKEapekUE0bsof4vjHK6hzapTNYGUJbnCUhb96MU1CAzIIdcwOg8F43bQwQvv0pilp_XFiQaxLHxHFzLbGYvtNgtL9WDqIKUjWvgyukrpDnn9kSofIMacyRam-0lR-DUibGnJCvrSDTY39dWzv9snNTd5fuCwhzy8sPZ2aDHWylixcOqsfDozqooHqmvEUC6g--w6PkIMMFaVgjl3A*2A2Fhttp*2A2A3A*2A2A2F*2A2A2Fsurfer.nmr.mgh.harvard.edu*2A2A2Ffswiki*2A2A2FBugReporting__*2A3BJSUlJSU*2A21*2A21LFqOYw*2A21tDBZFrn3IUiIYFmlM2uL6_tGbVoPuNqWs5ClV4bXYLiasR-ZsSbQP2scMUQqGzU2mRnDo0TdfS4yFw*2A24__*3BJSUlJSUlJSUlJSUlJSUlJSUlJQ*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQsIpGdmg*24__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaP6dcOkZg$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1v52XGgejgbw-sztjEJqwY4aZ3IfQHme2jIKM-FpjU7_jT2P7ji7iTzw4b4aQHSa-7r-LObu1Raq13RlqerbQ3OeRANo__;!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMrfICZvKA$

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Regards,

Xiaoxu

________________________________

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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1_a4tpkueHsjJfP9DeRjZRVyp9oJfzUbJws1ZIUddQEyNJb...<https://secure-web.cisco.com/1COzuvBzKpf4trvBIemSRX4PiRpu58WxfX3b5KHcTW7TaRD...<https://secure-web.cisco.com/1vUwgUf8_hfuWBdLjqYtf896YcElNEjV0u5cziIlwIYLAZh...https://secure-web.cisco.com/1VDcTwjjb22gvBWC4VubRD3aQBs7eEP7-LP-XJ1ciHiXUNQIZq9bUCaf8ZNH_XBDDcJ3F9SiPZIprg8aaHTiicteB2lIvo7727x-iqNr-z9EMh29EqsaPaU3cdDWfo3fZHrkIUmadcoxOTqjnMF7kMxgFTIJ6IaYo-iHzECdU3y3MOOUbUql2BUwI_OkubEfUcQ73ISFRgqrgScCN-GbrvwnXkwMVWcvXcTE1nf2-IfVIpU-2KbWjzRtiYnkFVN7LErtszAnMn2i-s-DZqGZeRLycR9pOtFn5VwtCehUoW02Aau-_X4prSYlHaIrcPY7A/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNREY32Wcw$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1hWSlhvM5pQaasr4kS03n7yvhP_WlnB5z6-aTjM7BhK4w2_c6hsuld3J28FcAoPcgavpI77HmdehVKEangCm-ATz9KZBx7IxffLerYb_RCaqK3OZoeyE_Ftl6VP_LCl8ouNMqSDgg6JTOEctZbKs1BDCKyv3vmig59Mef6QaWvPJqMeui-o0N4sI0E471EOz8Itm0S0ubdeAXjMf1lCy2OxHXQol4L3FAaJJsS-dijUG31XhL4bI6U6SEVyMs2U-uqcTTQis8HeOui5SEUg8quYL_fU8Vup-nSkRcKMPm0shwFqjNRl6lTa77jhwyNCZXYwxDwOt4jW7sxJ5qSY_Nmg/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNREY32Wcw*24__;JSUlJSUlJSUlJSUlJSUl!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaO2SH_yKg$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1_2fx82IMX_K0EdiMMMl83-aIqjBmXDwzR7PvKj1W-kHUzXpj2VG2LjAl92I69J0VeyS2uj4ybgt8b0PtU7haBXC3vQ5P-_iVQ30wZ_iw7S4aXSDjZH3UdWLNHPnSUlwO_PG-n-EfF7l42mhNBl_c7-G1GuZuAQpMI3NMxZZFT-tMH9JwvbXXsUc-dueM24rVmVqM-saSpxse4ng_NhKpsed1PAKRM6hicYYJp6RkeeE29n-VnKghzdpYTzQH-PCKlfBjkXIcJuRi6f4MHzYsvivReTCInxLVXcAkkLiRUI8ZKzau6QZZrzPDWx6kfsbm/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNREY32Wcw*24*253chttps*3A*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1hWSlhvM5pQaasr4kS03n7yvhP_WlnB5z6-aTjM7BhK4w2_c6hsuld3J28FcAoPcgavpI77HmdehVKEangCm-ATz9KZBx7IxffLerYb_RCaqK3OZoeyE_Ftl6VP_LCl8ouNMqSDgg6JTOEctZbKs1BDCKyv3vmig59Mef6QaWvPJqMeui-o0N4sI0E471EOz8Itm0S0ubde__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMrVtyTAcQ$

AXjMf1lCy2OxHXQol4L3FAaJJsS-dijUG31XhL4bI6U6SEVyMs2U-uqcTTQis8HeOui5SEUg8quYL_fU8Vup-nSkRcKMPm0shwFqjNRl6lTa77jhwyNCZXYwxDwOt4jW7sxJ5qSY_Nmg%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fmail.nmr.mgh.harvard.edu%2A2Fmailman%2A2Flistinfo%2A2Ffreesurfer__%2A3B%2A21%2A21LFqOYw%2A21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNREY32Wcw%2A24__%3BJSUlJSUlJSUlJSUlJSUl%21%21LFqOYw%21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaO2SH_yKg%24>><MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1fPtkwW_nmPu4_g8SZJ8Kwmg8lgobpLMXQFQVFzwnqYSSLJ...<https://secure-web.cisco.com/16Z744Elq_I6xPOH692yezQwBmnlsIlDwArz0HocA5bxiSw...<https://secure-web.cisco.com/1-rVoReJNPJ5ta1cKjQIgmV7VBVyFna-T8oZ2UYIdfM5_vb...https://secure-web.cisco.com/1r_2qe9us0rVHfwAnpjkuTsWF40r5eTcUMdlbTupVwR-v8eVJ16W9li-sBVYbpqzEeMKCTRurPBwh5qjQRreNEPEV3rWuVMYuRF9-PkMkLk4HhBtkCuEhCBXgmS0KgSaUOAhS_s_zOYvjQP_E17tYNN6hMzom1m5qBdaxYkh-h79qWeGxcLUDT6YkS3_HiLGjJUsSA9TV-FXf-aMpVoG24VrMtevCEJmKr8ZszDDxbXxryS4UPAMUou_N59wouz31n_Oiky8t-xTq0yfXSEeE-Y2iWBWrEsxKw2rz6T0kA16bbdTDHZjUKxvsRulaUPWB/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsecure-web.cisco.com%2F1V6ocVllnCV4qM28OYzTfXC4H1AurDYmNl4Chcjje22ASZZwdmj1vC2mZEyN3u9dNM6ZwXNkRZyiug_ERu7nnwi9nRkIuKt0MrfYN0aWkw-0xqVGNuNa1wXgwvJMwu9wOEiMd4rbkhk5a3Dp7RqPf-AYvvvfSIsE5uBzTBOWM7Cb40XJeKTUytEaN_fwCefswlxMxvuXgPeoHCTQsfDczQ2XVj73WjDaqUP4gwW7jQ6BwD0_JQJEojfkS6NHlbIciXUpcmmtbw4odNYq2ctRYiohaMybdk60bOKjEwj5UHEiRGHEVdQ1w3TCqipEf6seExi3_RkcW_XdayZlHWPt_wg%2Fhttps*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__*3B*21*21LFqOYw*21tDBZFrn3IUiIYFmlM2uL6_tGbVoPuNqWs5ClV4bXYLiasR-ZsSbQP2scMUQqGzU2mRnDo0QuRKXykQ*24__;JSUlJSUlJSUlJSUlJSUl!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNT-JrXhfA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1xXwK8NjrLcXMxDL4xnBgIHQNW4hpzdwiHzbV2pLLQcgIDv0E3PzrXlIQ1Qe2OkvGP3gM_1hifrJiVEDQ4LF1S8riFhTjDuYPAKu-eH7X54cBEQHlAoXegbA8ukNYIn2mx-TbMfLIDleHlCsOyIl2lwgWPfp4IVeLQS7jQR30snWtCC40iGiD4Qs6pHqIx3loyVzAsbyKS7Rf_ajL31Gc0HDxJaa-Dx6aqRhA4gs__;!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaNSELv5dA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1uoOu5HmGr-T-81FDU4sjIW0zG6Gv7ihkJtZRIcmLv4mAhiUwXsoxd7PAmpeOVCwFRIDf5nYLdoflBlAGe8ChO2rLsW8FuywCBwZ7tweiDJw14MD_59vWblrxSIurmrjHibCMzKm2fMzTAbDgrUczXxrflgwu4eDyty3AeC6JQ9h70dyjNH-xJcm2UvSXjNnDL__;!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMpaOnPn8Q$

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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1_a4tpkueHsjJfP9DeRjZRVyp9oJfzUbJws1ZIUddQEyNJb...<https://secure-web.cisco.com/1COzuvBzKpf4trvBIemSRX4PiRpu58WxfX3b5KHcTW7TaRD...<https://secure-web.cisco.com/1vUwgUf8_hfuWBdLjqYtf896YcElNEjV0u5cziIlwIYLAZh...https://secure-web.cisco.com/1VDcTwjjb22gvBWC4VubRD3aQBs7eEP7-LP-XJ1ciHiXUNQIZq9bUCaf8ZNH_XBDDcJ3F9SiPZIprg8aaHTiicteB2lIvo7727x-iqNr-z9EMh29EqsaPaU3cdDWfo3fZHrkIUmadcoxOTqjnMF7kMxgFTIJ6IaYo-iHzECdU3y3MOOUbUql2BUwI_OkubEfUcQ73ISFRgqrgScCN-GbrvwnXkwMVWcvXcTE1nf2-IfVIpU-2KbWjzRtiYnkFVN7LErtszAnMn2i-s-DZqGZeRLycR9pOtFn5VwtCehUoW02Aau-_X4prSYlHaIrcPY7A/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNREY32Wcw$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1hWSlhvM5pQaasr4kS03n7yvhP_WlnB5z6-aTjM7BhK4w2_c6hsuld3J28FcAoPcgavpI77HmdehVKEangCm-ATz9KZBx7IxffLerYb_RCaqK3OZoeyE_Ftl6VP_LCl8ouNMqSDgg6JTOEctZbKs1BDCKyv3vmig59Mef6QaWvPJqMeui-o0N4sI0E471EOz8Itm0S0ubdeAXjMf1lCy2OxHXQol4L3FAaJJsS-dijUG31XhL4bI6U6SEVyMs2U-uqcTTQis8HeOui5SEUg8quYL_fU8Vup-nSkRcKMPm0shwFqjNRl6lTa77jhwyNCZXYwxDwOt4jW7sxJ5qSY_Nmg/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNREY32Wcw*24__;JSUlJSUlJSUlJSUlJSUl!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaO2SH_yKg$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1_2fx82IMX_K0EdiMMMl83-aIqjBmXDwzR7PvKj1W-kHUzXpj2VG2LjAl92I69J0VeyS2uj4ybgt8b0PtU7haBXC3vQ5P-_iVQ30wZ_iw7S4aXSDjZH3UdWLNHPnSUlwO_PG-n-EfF7l42mhNBl_c7-G1GuZuAQpMI3NMxZZFT-tMH9JwvbXXsUc-dueM24rVmVqM-saSpxse4ng_NhKpsed1PAKRM6hicYYJp6RkeeE29n-VnKghzdpYTzQH-PCKlfBjkXIcJuRi6f4MHzYsvivReTCInxLVXcAkkLiRUI8ZKzau6QZZrzPDWx6kfsbm/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNREY32Wcw*24*253chttps*3A*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1hWSlhvM5pQaasr4kS03n7yvhP_WlnB5z6-aTjM7BhK4w2_c6hsuld3J28FcAoPcgavpI77HmdehVKEangCm-ATz9KZBx7IxffLerYb_RCaqK3OZoeyE_Ftl6VP_LCl8ouNMqSDgg6JTOEctZbKs1BDCKyv3vmig59Mef6QaWvPJqMeui-o0N4sI0E471EOz8Itm0S0ubdeAXjMf1lCy2OxHXQol4L3FAaJJsS-dijUG31XhL4bI6U6SEVyMs2U-uqcTTQis8HeOui5SEUg8quYL_fU8Vup-nSkRcKMP__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMr_6rV3Ww$

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1D79kOUcMdPTXdhZcXlugM1bEvwo12AtfLxWCvK1S7jb8s0...<https://secure-web.cisco.com/1sMA2VlMI9NSBYTumCEFbqt3y2e9XRp12sxy8MIb-1DyTfs...<https://secure-web.cisco.com/1C9zN6Lu6OzJkCQsZuMIJkLT12oGE6nkOEYvpjjMMhb-l4B...https://secure-web.cisco.com/10pm6u-N3DtmMCzEZf3wbwSn1lnXPo99xiyb-g31uoq1e3_8e9-5cYZpQ1yY5JIIDQ4cxaqNgLD_AZw_lv1i6gxumRhmip6_T30_FdPdqATgV37uG5dTtXB64zhqPbdkSvZ0rxQrIQawp9VjjFip8yLYm7rlJNqxMKV_8pk14rUcf_kmDUrPYws6KztgyPk-QyBp3XfIbc4HJujRSTv4jj1_X9YwuQESsXSZlJOi9CN7D6GEqm9Ud7jCKB3nxXsx_r7HI4GibrxOeLvX7qDE8LlLVv902oCogltonIMSBKtVt4B7ReWsGPq9GBSoaEKFp/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fwww.massgeneralbrigham.org%2Fcomplianceline__;!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNSr2YmNpQ$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1pmYJlv7pYtwSgJ1htPUDuaTt6BradzfcbgiSEU3HBwyEAZKOem75exFE3f2vb8kvcjkgvxuPlW9tQx116cCX4o0r1Q8ZU_6uPvWMHjUnHT8HhsTipcbyYVSTv-qCdId_QA9DRCm7NslHScf-kcsexuOfKQB5H2Z3i-yKCc63gerAMA9M6kqDdLjK_iRhG_wb9annUrEtAXwxJVOYc67_RPiZhFc9Nmt9NL80j1nhChH8e8chRNRteirc-PW1n_90dOyPii0nf0cwDTZY0ZB_7Lfx6Be79KFr18OWVuZEww_gmgO0j2GTZKTjDcu5yZaAA8Z64-U-xdCSTSiXNBpZgw/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fwww.massgeneralbrigham.org*2Fcomplianceline__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNSr2YmNpQ*24__;JSUlJSUlJSUlJSUlJQ!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaO11J3tAg$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1ZHG-L3Fp9xqPxSDeJvkSbtvBN-uPjZsV0TBqm1IAcyZ6p9iOyDE0J9nFP0Yf7vSF3uydjIY-ICn7hMhzvjhM5agU5hxZcfFsdOt3IBpRo6Nxguj7eli1c3oGGj1QA9BDvrXpReofFaYx_YIAXI6fEj3ajPjS6LofT0tdthgcI5FfI8-kkFIYplrH5yNHVNl85GftizuiAVp16WzadohI-lUUoCkZxqFiHPYEgMFzpRhLBQ5NyekaDo5nvJlYarm9r0WM7vcy_3yZUcpKIQpUdJTNBiGEKs6nNlpUOjsoyxCLihauHMtlvDJDzRQfMVQW/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fwww.massgeneralbrigham.org*2Fcomplianceline__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNSr2YmNpQ*24*253chttps*3A*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1pmYJlv7pYtwSgJ1htPUDuaTt6BradzfcbgiSEU3HBwyEAZKOem75exFE3f2vb8kvcjkgvxuPlW9tQx116cCX4o0r1__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMpDu9mtwQ$

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Freesurfer@nmr.mgh.harvard.edu

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Unfortunately, we don’t, that’s why I was thinking of building a container with MCR. I’ll check how our matlab admin would respond to my license server request to check if I can license it correctly in a container. Thank you Paul!

Regards, Xiaoxu

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Wighton, Paul Sent: Thursday, December 7, 2023 12:17 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

It matlab available on your HPC? If so, you could try mounting it into the container. -Paul ________________________________________ From: freesurfer-bounces@ nmr. mgh. harvard. edu <freesurfer-bounces@ nmr. mgh. harvard. edu> on behalf of Na, ZjQcmQRYFpfptBannerStart This Message Is From an External Sender This message came from outside your organization. ZjQcmQRYFpfptBannerEnd

It matlab available on your HPC? If so, you could try mounting it into the container.

-Paul

________________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Na, Xiaoxu <XNA@uams.edumailto:XNA@uams.edu>

Sent: Thursday, December 7, 2023 1:12 PM

To: Freesurfer support list

Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

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Thank you so much for your confirmation, Paul! Then I guess I need to shove them back to my work station to continue if I couldn’t put a full matlab into the container. Thank you for saving me the time trying the mcr!

Regards,

Xiaoxu

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Wighton, Paul

Sent: Thursday, December 7, 2023 12:09 PM

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu>

Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

It looks like mris_compute_lgi won't work with *any* mcr and needs a full matlab installation. Sorry :( -Paul ________________________________________ From: freesurfer-bounces@ nmr. mgh. harvard. edu <freesurfer-bounces@ nmr. mgh. harvard. edu>

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It looks like mris_compute_lgi won't work with *any* mcr and needs a full matlab installation.

Sorry :(

-Paul

________________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Na, Xiaoxu <XNA@uams.edu<mailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto:XNA@uams.edu>>

Sent: Thursday, December 7, 2023 1:00 PM

To: Freesurfer support list

Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

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Hi Paul,

Thank you so much for your confirmation! This is exactly what I’m having trouble with. In this case, maybe I can’t go with 7.3.1 and upper, I can go back to work with 7.1.1. Have you tried with 7.1.1 with mcrv84(matlab 2014b) running correctly? Last time I run LGI was on my own workstation with 7.1.0 and full matlab 2018b installed. Since I want to run all subjects on HPC this time, I have to build a docker to support that. If you have any version of freesurfer-mcr pair that is working for LGI, will you please kindly let me know and I’ll give it a try too? Thank you so much!

Regards,

Xiaoxu

From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>> On Behalf Of Wighton, Paul

Sent: Thursday, December 7, 2023 11:54 AM

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu>>

Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

I just tried this in a container. It looks like `mris_compute_lgi` is not designed to work with the mcr, and needs a full matlab installation. I started by jumping into a freesurfer 7. 3. 1 container. ``` docker run -it --rm freesurfer/freesurfer: 7. 3. 2

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I just tried this in a container. It looks like `mris_compute_lgi` is not designed to work with the mcr, and needs a full matlab installation.

I started by jumping into a freesurfer 7.3.1 container.

```

docker run -it --rm freesurfer/freesurfer:7.3.2

```

Then I installed matlab mcr

```

fs_install_mcr R2019b

```

Note the output `fs_install_mcr` says:

```

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

/tmp/tmp.AzujBUG5W7/install-target/v97/runtime/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/bin/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/sys/os/glnxa64:/tmp/tmp.AzujBUG5W7/install-target/v97/extern/bin/glnxa64

```

But this is what should be added to the `LD_LIBRARY_PATH`:

```

export LD_LIBRARY_PATH=${FREESURFER_HOME}/MCRv97/runtime/glnxa64:${FREESURFER_HOME}/MCRv97/bin/glnxa64:${FREESURFER_HOME}/MCRv97/sys/os/glnxa64:${FREESURFER_HOME}/MCRv97/extern/bin/glnxa64:${LD_LIBRARY_PATH}

```

And I can confirm the `mris_compute_lgi` indeed does not work:

```

mris_compute_lgi --i $FREESURFER_HOME/subjects/bert/surf/lh.pial

ERROR: Matlab is required to run mris_compute_lgi!

```

But it looks like the mcr was installed:

```

find $FREESURFER_HOME/MCRv97

```

The error is a result of `getmatlab` not being able to find the matlab binary, which isn't included in the MCR.

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1NoJp46Vwsb_z1VO5WAUPMccbaXF1epUZF8KKHPIs-oZYjx...<https://secure-web.cisco.com/10op4brc_zgddxXMyVdSfWCgE6yvxy1dd4V9LZZ_ryNMZ4Q...<https://secure-web.cisco.com/1K3dsrxLWI05IezScxTQl5iw6JRqHJ9Hh_jMzS-ryJ_Cw-m...https://secure-web.cisco.com/1g6K84blVnxUlSBSgoGcMjg-1Hkbwvdm0FDeufPAc5LbaOOSkYFSCYtZQSlm0MMA2I6Rwgp5kcxpAoscb55KgDXr67USK404NZT8wlSGGwYXRy-TJNsZbpSh_VPwIe2bmo6-WZClY8JNJP2NgKdZgxBkDAZJY_n_7WT6AY4fOuo6cSlSdkXKBWhbIw9oOkUdLRh-QHAL_uoK9EaLBuu76Tpk43DImjgXRhUDWluNZ77kLN3V217iHFrzi1rj_jikL4R0hpIsrKMCbPnH9ANqNsNcFZhUEpwWKsicojmmHKyibG_XSxnVVbTn-qiYh2JzbybfWpYvzLyxDlMg6kQesqA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2F5b2abcc5b65f7bca3e96f7c2e05d0da5531b5e03%2Fmris_compute_lgi%2Fmris_compute_lgi*L56__;Iw!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaO-Pl2JeA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1mYopLjr-lDIhMqYAqXF2VHCgLxTBzZfleAFg7ZLuPtenUy8m-FJ0KVOpf0ohKzuXa0PM16X6BLRIWEEQI2GAaRZPKAUyMXRzGUSYevad3oYqWzEcxs_obEHuL3FdSvJC4LMBAuTwNTQzMnO1n3Nb0YwdWtTjVpU5eCJ6fa0lTd4G8nJhBEzH7LVDCxkc7mughRdxr7zJlwnB33a_E1MYnWoTL4TzjKIVRJGl6E59M2D7sbio7tqySiofNC5a4cEaTXaMv4epFq5UW20WfwofMsAfyD1KUagZ15d9P7VsHbV1F_JfC4NdeCr_olYxxUCc/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fgithub.com*2Ffreesurfer*2Ffreesurfer*2Fblob*2F5b2abcc5b65f7bca3e96f7c2e05d0da5531b5e03*2Fmris_compute_lgi*2Fmris_compute_lgi*2AL56__*3BIw*21*21LFqOYw*21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaO-Pl2JeA*24__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMqd542cbw$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1mK5Lhsre_q4PYjQCTk7nn4PE4JvlWrYQ4MNDwWFp5atGuGC_JNuCIr6vrCh0HhD6X-ur2FYyU1LecmwpKgOgzXMwH6wdkHava2l9_eXjUQHxp41N57lb87Lx8dAESGwErK7-tBAeRfmCBFqpbUkIVk6T4Qf8q2gB_mIhWdCTH86DyLDFNoGYHv2_pVnsyek6beNlKlbIfEvAQBcJqYFL0d-hnrg9wDqd7KO8_uHMlWIpzFqKrLL_ymWQI6ekZJiCW0yP891UDcFL7g04U3hcNe-O06hl4M8gGwP257_v3rfauHf3zFf_ktRGgonT_geY/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fgithub.com*2Ffreesurfer*2Ffreesurfer*2Fblob*2F5b2abcc5b65f7bca3e96f7c2e05d0da5531b5e03*2Fmris_compute_lgi*2Fmris_compute_lgi*2AL56__*3BIw*21*21LFqOYw*21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaO-Pl2JeA*24*253chttps*3A*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1mYopLjr-lDIhMqYAqXF2VHCgLxTBzZfleAFg7ZLuPtenUy8m-FJ0KVOpf0ohKzuXa0PM16X6BLRIWEEQI2GAaRZPKAUyMXRzG__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!LFqOYw!rJFAzZ4pXQ79Dmu5mIEef8olXY__W0USXDul-P8YbOdN3Gy4MGbG934CwKf4Ha6W_i1WFMbMj1eklryWZr29aw$

USYevad3oYqWzEcxs_obEHuL3FdSvJC4LMBAuTwNTQzMnO1n3Nb0YwdWtTjVpU5eCJ6fa0lTd4G8nJhBEzH7LVDCxkc7mughRdxr7zJlwnB33a_E1MYnWoTL4TzjKIVRJGl6E59M2D7sbio7tqySiofNC5a4cEaTXaMv4epFq5UW20WfwofMsAfyD1KUagZ15d9P7VsHbV1F_JfC4NdeCr_olYxxUCc%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fgithub.com%2A2Ffreesurfer%2A2Ffreesurfer%2A2Fblob%2A2F5b2abcc5b65f7bca3e96f7c2e05d0da5531b5e03%2A2Fmris_compute_lgi%2A2Fmris_compute_lgi%2A2AL56__%2A3BIw%2A21%2A21LFqOYw%2A21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaO-Pl2JeA%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJQ%21%21LFqOYw%21vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMqd542cbw%24>>

The `getmatlab` script:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1UTqP-MvbC4mBcGkTtcbCo3KpkJwr1oOBuTfdU2p3RsaTda...<https://secure-web.cisco.com/1a9MboG32w5WZivuiEvpmop0a__AmT4AxM6-vwg717JiPqc...<https://secure-web.cisco.com/1k9bi6miTCVhgd45cPQNjc9t8ZUuID-IPBcqW1CuBj0aO8R...https://secure-web.cisco.com/1z5S9EnB-KS-Lqwg-PSWbaeF_wa15zMMONCv-zPmD-Pof4vSULFRg3BEaJ3P6dw4-CTYdDx2y7mdBTkZxO-wAj5Mhr2ABOLgmsCQG0dNXt6E7Me2Vfsk7vPm5FtdQ5sfDmZfaFBEHEUFXzTgs92hq5IEvbm6AKsdQz_4oJ-WmRf5itFQIm9hkieb0cHg0usEglFgy4ymUM5AV5S3gQ4jneJefQi_sjAL9bGch0YZmYhPijGYoP8x_667rMMNkPWGXJaRwjkpp4q9jVVrEoeDnIh9lzRpyNiHyQoM2pOgOY1b0d1TRMpNBt-RioNJd-g0SKV_BX0rH-q-O5Ywbt3WY8g/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Ffsfast%2Fbin%2Fgetmatlab__;!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMQkTmFpg$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1iNn3UfSzhaLRI-ytx34ot5LUf_9_o6epLcaHVHfPyUkcpaoWz7o3NWK7CrzfMOuamuLMhlTzb4YuDmGv0wiGNXydK-QnYr8rjPcD4s9JBY5cC_KNwoocXV_fK0m487N2l2XR4qx_pbHqL0ow-dSNmmYYzgVSNwXL4QPcqfvTfm6bbcf2l9S2lQdHAU_4udFIGOwIzCtwCdqUB7dnhh4MshqJpFav0oYbCVwv4Oosdbo1md0qKf4d48vpJdKGoxCaL6cHa1lKnL072kxi1seMwjTMguWxJsQ0ys9LfY3W6ZsMGXt3TBi_g26cYJCTlJ05/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fgithub.com*2Ffreesurfer*2Ffreesurfer*2Fblob*2Fdev*2Ffsfast*2Fbin*2Fgetmatlab__*3B*21*21LFqOYw*21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMQkTmFpg*24__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMo-rT_xeg$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1l5WsNcSnSfyxXot0_Mn8OueR6-Hubb-FaJei9lTSEYU-RB5nMruSX7w6_Ops1JLkaSCv37oTqeE-ZMZNmsYxyeclicvxyCWXDuXuofN4__jeipRGfqzCkOCbpA302x-8zerlqoqKi2eoyQSVn1gauyqtV3oXIrAvVqX9DpSp5-AnPX2ZRiPGZYmgyiMNLuVC4Z7ynrhlXqHaTN-3eNT3r2KruETB9DFiZlNJLa8jqrej7JsEPUiRJz0bFgFLd3dJ6J1vyidnNRl6atVB8n6NyP-y3ptpj8rqXo_q7ZOgd4CcX2GHvyTSOXmc-YW8LCEa/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fgithub.com*2Ffreesurfer*2Ffreesurfer*2Fblob*2Fdev*2Ffsfast*2Fbin*2Fgetmatlab__*3B*21*21LFqOYw*21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMQkTmFpg*24*253chttps*3A*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1iNn3UfSzhaLRI-ytx34ot5LUf_9_o6epLcaHVHfPyUkcpaoWz7o3NWK7CrzfMOuamuLMhlTzb4YuDmGv0wiGNXydK-QnYr8rjPcD4s9JBY5cC_KNwoocXV_fK0m487N2l2XR4qx_pbHqL0ow-dSNmmYYzgVSNwXL4QPcqfvTfm6bbcf2l9S2lQdHAU_4udFIGOwIzCtwCdqUB7dnhh4MshqJpFav0oYbCVwv4Oosdbo1md0qKf4d48vpJdKGoxCaL6cHa1lKn__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!LFqOYw!rJFAzZ4pXQ79Dmu5mIEef8olXY__W0USXDul-P8YbOdN3Gy4MGbG934CwKf4Ha6W_i1WFMbMj1eklrxFoq-63Q$

L072kxi1seMwjTMguWxJsQ0ys9LfY3W6ZsMGXt3TBi_g26cYJCTlJ05%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fgithub.com%2A2Ffreesurfer%2A2Ffreesurfer%2A2Fblob%2A2Fdev%2A2Ffsfast%2A2Fbin%2A2Fgetmatlab__%2A3B%2A21%2A21LFqOYw%2A21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMQkTmFpg%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJQ%21%21LFqOYw%21vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMo-rT_xeg%24>>

-Paul

________________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>>> on behalf of Na, Xiaoxu <XNA@uams.edu<mailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu>>>

Sent: Thursday, December 7, 2023 12:03 PM

To: Freesurfer support list

Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

External Email - Use Caution

Thank you Paul! But I have already updated my neurodocker to the latest. I’ve tried to create a link using the same way you’ve listed below, and it didn’t help. In this way, I feel the mcr was not fully installed as I couldn’t locate the file MCRv97/bin/glnxa64/libmwlaunchermain.so, that’s why I turned to the official way, which installed a lot more files in that directory, but still not working.

The official way that R suggested, I feel like the script fs_install_mcr has already remove the temp it created during the installation once exit, so appending that to $LD_LIBRARY_PATH didn’t help. Any other tricks? Thanks so much!

Regards,

Xiaoxu

From: freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>>> On Behalf Of Wighton, Paul

Sent: Thursday, December 7, 2023 10:35 AM

To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu>>>

Subject: Re: [Freesurfer] Freesurfer 7.3.1 MCR 2019b

Hi Xiaoxu, This is how I built a FreeSurfer 7. 1. 1 container with matlabmcr 2014b (https: //urldefense. com/v3/__https: //github. com/pwighton/fs-docker/blob/master/notes/20201127-fs711-neurodocker-min. md*freesurfer711__;Iw!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g$)

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Hi Xiaoxu,

This is how I built a FreeSurfer 7.1.1 container with matlabmcr 2014b

(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1nj8xBb118LGSu-mLOnl4y_IPteoyYyRDN4h98wzI5FXzLM...<https://secure-web.cisco.com/19Iof1D0xj0l5Yl91b4kGURw9xp0xYhdU4eBeDo5z7Wa4Jj...<https://secure-web.cisco.com/10tEEBObqGnn0AmG1CksyaKvBurcNGhni4XG49zunXiJdik...https://secure-web.cisco.com/15qp4FJ2G07XS9-t-J6zsoqcX4-LDGqEznKDwmZH9V3JXoMq33rgJOlyGwV9mYWQBdPN40fJ0KUWY0lapAYkGQyGV4thbhIUWr6DyLf5fgZmJYfqvJT8EOBDFsqOdbEiNrkT5Zpjij9D0291hsUI82uxHuQVq2CUVbc3h3o1AQauVrS8tRAoRVcti_EawwEPqY_-0L2ubQg_aWx5oC-QlpOsnS-qO1ueJ-gFEpe0cKPPSmnfzM9Omkjh6-2vSHSveWw1ZZP0eeJ76X8nfVNJSMkYtrOfAhdHnR6jHOKJVT17FEbsL62OzHl97U_IniPMNEd34v1sh_YDOcGnYD7kEOQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fgithub.com%2Fpwighton%2Ffs-docker%2Fblob%2Fmaster%2Fnotes%2F20201127-fs711-neurodocker-min.md*freesurfer711__;Iw!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1KnnY8C5yTwrcARPclPPQqXaaF2UoxOeMqo5RQ4nwHj-68EbpR9U7X4dt88a3AFmGhyRRXTNll8XcHMzmIyiGyG-ndBLJzVgG2u56B2XGnM6nSQ0xLfeA2M8TeEz9oV8rEyDFKOur8CdGoNC6LLNYh9A8EJCV94l11edqMjtUkD35prfRNdeFFMPSgOEpvHyZHEaB7Hb9gntithqZrd0RaI6-CXM42edJaEuft1MqzhpKt6QlAm7yfDFmgBkFs2pyYkEVgPjYBKdPS4nafzy0nboAHyzt0PekaKfI8hWBZbI43Ray_nllXVobBZ4xc9lAMlZMylvy_66zSwcvv8-KbA/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fgithub.com*2Fpwighton*2Ffs-docker*2Fblob*2Fmaster*2Fnotes*2F20201127-fs711-neurodocker-min.md*2Afreesurfer711__*3BIw*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g*24__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaOmqycPgw$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1dUdGOnyUbe5ym9j50T4tZkX-u9ssHpZ19OScWxIyEZP9ID2nzod64oZP619RWSJCgvD2H10XGWwBDNBTTJoM6vSr0z4j_c1prFqOBBAYjnkq9VlN4n3ys0xv_ennA0JOOv-aUCRLJyYQAHVVr4h3-G2VRtNcCNvDtaZ1LT62zupb2c1Kt8m5ubUlHs3VMhLWi6pd_rkOaMt_VJc05CeJRri3xYRnZMqR2tPXovfCwcFq2GmWi_cpV5IIAe-DzjwXa9NJkBKWSwFjaEAIjwmmMGdpOKIWA0l_V6oq7EhlSXxNLZKXEwn55QuyDQ6lt88r/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fgithub.com*2Fpwighton*2Ffs-docker*2Fblob*2Fmaster*2Fnotes*2F20201127-fs711-neurodocker-min.md*2Afreesurfer711__*3BIw*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g*24*253chttps*3A*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1KnnY8C5yTwrcARPclPPQqXaaF2UoxOeMqo5RQ4nwHj-68EbpR9U7X4dt88a3AFmGhyRRXTNll8XcHMzmIyiGyG-ndBLJzVgG2u56B2XGnM6nSQ0xLfeA2M8TeEz9oV8rEyDFKOur8__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMo2xLMsTA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/18

lPPQqXaaF2UoxOeMqo5RQ4nwHj-68EbpR9U7X4dt88a3AFmGhyRRXTNll8XcHMzmIyiGyG-ndBLJzVgG2u56B2XGnM6nSQ0xLfeA2M8TeEz9oV8rEyDFKOur8__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMo2xLMsTA$<https://secure-web.cisco.com/1EyauXZJxFZ-SNh_elCqxUCW8lkMCIXc4HPZCYqbiCsJZaF...https://secure-web.cisco.com/15qp4FJ2G07XS9-t-J6zsoqcX4-LDGqEznKDwmZH9V3JXoMq33rgJOlyGwV9mYWQBdPN40fJ0KUWY0lapAYkGQyGV4thbhIUWr6DyLf5fgZmJYfqvJT8EOBDFsqOdbEiNrkT5Zpjij9D0291hsUI82uxHuQVq2CUVbc3h3o1AQauVrS8tRAoRVcti_EawwEPqY_-0L2ubQg_aWx5oC-QlpOsnS-qO1ueJ-gFEpe0cKPPSmnfzM9Omkjh6-2vSHSveWw1ZZP0eeJ76X8nfVNJSMkYtrOfAhdHnR6jHOKJVT17FEbsL62OzHl97U_IniPMNEd34v1sh_YDOcGnYD7kEOQ/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fgithub.com%2Fpwighton%2Ffs-docker%2Fblob%2Fmaster%2Fnotes%2F20201127-fs711-neurodocker-min.md*freesurfer711__;Iw!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1KnnY8C5yTwrcARPclPPQqXaaF2UoxOeMqo5RQ4nwHj-68EbpR9U7X4dt88a3AFmGhyRRXTNll8XcHMzmIyiGyG-ndBLJzVgG2u56B2XGnM6nSQ0xLfeA2M8TeEz9oV8rEyDFKOur8CdGoNC6LLNYh9A8EJCV94l11edqMjtUkD35prfRNdeFFMPSgOEpvHyZHEaB7Hb9gntithqZrd0RaI6-CXM42edJaEuft1MqzhpKt6QlAm7yfDFmgBkFs2pyYkEVgPjYBKdPS4nafzy0nboAHyzt0PekaKfI8hWBZbI43Ray_nllXVobBZ4xc9lAMlZMylvy_66zSwcvv8-KbA/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fgithub.com*2Fpwighton*2Ffs-docker*2Fblob*2Fmaster*2Fnotes*2F20201127-fs711-neurodocker-min.md*2Afreesurfer711__*3BIw*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g*24__;JSUlJSUlJSUlJSUlJSUlJSUlJQ!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaOmqycPgw$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1dUdGOnyUbe5ym9j50T4tZkX-u9ssHpZ19OScWxIyEZP9ID2nzod64oZP619RWSJCgvD2H10XGWwBDNBTTJoM6vSr0z4j_c1prFqOBBAYjnkq9VlN4n3ys0xv_ennA0JOOv-aUCRLJyYQAHVVr4h3-G2VRtNcCNvDtaZ1LT62zupb2c1Kt8m5ubUlHs3VMhLWi6pd_rkOaMt_VJc05CeJRri3xYRnZMqR2tPXovfCwcFq2GmWi_cpV5IIAe-DzjwXa9NJkBKWSwFjaEAIjwmmMGdpOKIWA0l_V6oq7EhlSXxNLZKXEwn55QuyDQ6lt88r/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fgithub.com*2Fpwighton*2Ffs-docker*2Fblob*2Fmaster*2Fnotes*2F20201127-fs711-neurodocker-min.md*2Afreesurfer711__*3BIw*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g*24*253chttps*3A*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1KnnY8C5yTwrcARPclPPQqXaaF2UoxOeMqo5RQ4nwHj-68EbpR9U7X4dt88a3AFmGhyRRXTNll8XcHMzmIyiGyG-ndBLJzVgG2u56B2XGnM6nSQ0xLfeA2M8TeEz9oV8rEyDFKOur8__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMo2xLMsTA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/18

MGdpOKIWA0l_V6oq7EhlSXxNLZKXEwn55QuyDQ6lt88r%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fgithub.com%2A2Fpwighton%2A2Ffs-docker%2A2Fblob%2A2Fmaster%2A2Fnotes%2A2F20201127-fs711-neurodocker-min.md%2A2Afreesurfer711__%2A3BIw%2A21%2A21LFqOYw%2A21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g%2A24%2A253chttps%2A3A%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fsecure-web.cisco.com%2A2F1KnnY8C5yTwrcARPclPPQqXaaF2UoxOeMqo5RQ4nwHj-68EbpR9U7X4dt88a3AFmGhyRRXTNll8XcHMzmIyiGyG-ndBLJzVgG2u56B2XGnM6nSQ0xLfeA2M8TeEz9oV8rEyDFKOur8__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl%21%21LFqOYw%21vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMo2xLMsTA%24>

CdGoNC6LLNYh9A8EJCV94l11edqMjtUkD35prfRNdeFFMPSgOEpvHyZHEaB7Hb9gntithqZrd0RaI6-CXM42edJaEuft1MqzhpKt6QlAm7yfDFmgBkFs2pyYkEVgPjYBKdPS4nafzy0nboAHyzt0PekaKfI8hWBZbI43Ray_nllXVobBZ4xc9lAMlZMylvy_66zSwcvv8-KbA%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fgithub.com%2A2Fpwighton%2A2Ffs-docker%2A2Fblob%2A2Fmaster%2A2Fnotes%2A2F20201127-fs711-neurodocker-min.md%2A2Afreesurfer711__%2A3BIw%2A21%2A21LFqOYw%2A21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQur45w9g%2A24__%3BJSUlJSUlJSUlJSUlJSUlJSUlJQ%21%21LFqOYw%21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaOmqycPgw%24>>)

```

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-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>>> <freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu%3cmailto:freesurfer-bounces@nmr.mgh.harvard.edu>>>> on behalf of Na, Xiaoxu <XNA@uams.edu<mailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1rt1YtfHh4XlSiwG68TcMJ91IR09LVfLg8tsZVDwlipbmKq...<https://secure-web.cisco.com/1bNGpGOTAND8Wq1UdbAnSnxAQdb_fRCU_9aKUuYtaaaldMo...<https://secure-web.cisco.com/1gw19JJdXeeyzHmzwhtTu2vnf0uClwX3yJXKZ1YQi3DQqBb...https://secure-web.cisco.com/1el5uOumhLMir_zrAWFEgOCkfd_60AK_ewQEr7S4c5ii30TYQnv-x-yoY2wR6-0VYY-F9TxKy6dlRv-lgHzHbovWRW7MTdvuuPEP5Ep4HhkobzWx2ntumME6OxEGpqxh6Kbr_sesgnZHE0LwvWix2OeSy4MMyoVfPICQlqENhuAlorvliz8urSt0wdYdarxQ22OxOfGt8Jaa-Lg7V0DPo9aj1SkBcCRQfAjnbypebPDe7laG4qB6LW4bHfXR9mDV3engrR84HkcqoFFxIer9WLqoM_q0Ak-CNVxBJjf2JIP3CxkV9ZcZGVs3KMhTW7Ur2DQdsYtO3ngYMj6I0qyW0xA/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting__;!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1OaUQzJNRPo049e0G3gE7Svl2Z8-MWvMQ6O-8qzfk_20N7GLezlIKD7mW0K1Ee7_c_6_2zewxx7Iib8Knm_tTL-cwpOHfT5qvJpf6mdcuxX03P9uRuE0s-bZ3b3fBVSVbsf6nqSmmLShMDwtuliQ3EwTiON8GQMaC0ZKvHvkTjFXe4IFB_-2pMbktHuXm1MQQzrjpyu57CSZ_5u9tF8A9NRO47FkqmqYqwZo-DOyb0w5MeElRYx2c6By4DouUz8gziaDzP-eD4PbkttUmev26M3JGIRa1iTd82WeCZHoUh5z3TyDK0EkffTZjxw4YHz84OSP-IHY0DMYXF7QxBb49qw/https*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FBugReporting__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA*24__;JSUlJSUlJSUlJSUlJSU!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaN-J8pIDQ$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1XQCbKYk8dPlPndcc-CWngT1LMlXOkav_qc5WZkzwS1_W8nGf1ewc1odzRecVmXVbCdTtHWBWPEhTynwSihjw9zIm9vI7_ok39sPyY25kL8ZcrKLGKefqQhcFcZ7jRb6UHQ58824zswlD6khQ-wIoBG_s8Vn1tNNlWg1D8tu81SiOGE9ehQuikt3h74iAKqnusd1GyLWfrlkvVo2Qrut1qCWDPfvIIVv4-Dx2fx78k3rSdqeE2wG-M-9Z5Hh7cCx0b0FEyD4JPcRtY_pnDB-KJFJ6_TGMlKBxOUSHXQRkfUt1JjL-YhvfIKrL5VlxvDdL/https*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FBugReporting__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA*24*253chttps*3A*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1OaUQzJNRPo049e0G3gE7Svl2Z8-MWvMQ6O-8qzfk_20N7GLezlIKD7mW0K1Ee7_c_6_2zewxx7Iib8Knm_tTL-cwpOHfT5qvJpf6mdcuxX03P9uRuE0s-bZ3b3fBVSVbsf6nqSmmLShMDwtuliQ3EwTiON8GQMaC0ZKvHvkTjFXe4IFB_-2pMbktHuXm1MQQzrjpyu57CSZ__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMp1xOZ-wQ$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1Trtx7sidR3RBuLtO_V__UW62fB-2m0kP9x8DQyEE0eBMQwcQI7mzS3ScR2UKvpVFESfcXgy2uoF28DkjM-IXa6SUTWHCyXEmAe0GVgWYB8fbgz8hwEsQ3yQt6yY7

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finish

From: fsbuild <fsbuild@contbay.com<mailto:fsbuild@contbay.com<mailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com<mailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.commailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com%3cmailto:fsbuild@contbay.com>>>>

Sent: Wednesday, December 6, 2023 9:14 PM

To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu%3cmailto:freesurfer@nmr.mgh.harvard.edu>>>

Cc: Na, Xiaoxu <XNA@uams.edu<mailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@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).

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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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1OifRFBy7y3q-9gG7P7c3maXZcN7oZH9WETb3gMgpr6-LMF...<https://secure-web.cisco.com/19tjHE2DE6sVSUFIk30Hg5A-PLmDPhZeV5mBnynnxmcGTwq...<https://secure-web.cisco.com/1Nq2inDQcKI5n3JMfst7nbC4LhDmXtLLmib_T8fU2ZSn3qO...https://secure-web.cisco.com/1MdMfuEkYvvTEEBUtYCrF0pryo6Z-FGZ2orlQy-SKBGaaP9NQKcbDjiEeqQB856h6WyebbsTscevv62uzr1WVeD7nrKqshZazZ9JRQu16u2tBKQqlINSOxHgll4VI06lxt9vckmCfEvSHo6-JAyKjLId3NnqdlDOOacPjW1Bee7QqLNBA0gT_srBaHNwDthGVWnsOaGH3FRA92VQQV3K1rVg-fAaLwry7Rhu_HyLH5bj6S54kGL-m9EEq86fC0Bt2ZARHyzkTN3yKzl5JBWWjhTbhYcRMIcURf0CoDBBVXD5m-gNFye-ZH6xlSEKMAvgrNCjvpzZlG090iYM_ivpkVA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads__;!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQK2zaIeA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1J2CTZgiRcJrmtg5-7SfglDGEjwy8yt7335FB1LJGFTRe_drJNuSccrm-Yw9q3TwPPk9nBbsxMTVuDEMe64WpPbafz_pTt8BA7gBz-OPH6GQApL1oIpDgYevwzGQITPfJ1CQ235F2x69va42WvhKnwIOr2J2VN9JnFRYBEzr3znk8Equed0wTIzGU-mERXdKoFGTBTNTcSCy_OWv6B4TX914xTQh2Opm5nQB18d4Seu7hH8fUGxfhYEsWvphUvYYTrw7s42TcYU0qwM9XwbSmi8WDFUktpTM4xIhxgWzRiJEOQncbcltVQAxdVCKDqQo55NGAsxbsImeOdMDpsf8Tvg/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2Frel7downloads__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNQK2zaIeA*24__;JSUlJSUlJSUlJSUlJSU!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMrCbA6nA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1YcV6Y1tdz08V8rqoFceWLuOmHKpNTfhJbfW5LYtXrwCGjKsuOII75kS1Bf-doQC6sCoIIJjf6cNLO3HJ1pzrTmSa1yKdhB-n7k0YjxbqzflMRDAfIf8oG9n1tKWNBBimHR1OwepG63jv0UsHzT9e3MVJm5onsFbzL_OMairlifJwedhw3Z9w3rxu8affDgHdjx_iLdhsUGmvfHQzyfHypelsIjR53FeRe8unCW0cMucTwK60qQiQ0_ztOZCEcZUtWKTY5MetrcszeyuKD3OrtJljxPLx0WTp60_9P5NfX8ZmH9z-UbvXBvsW1SvgXHIM/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2Frel7downloads__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMd__;JSUlJSUlJSUlJSUlJQ!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMrJ96KQWw$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/13yGMMlOUqNKyUjIDIs7lg10zl1XBycjcn--88UkwjC9obYefnWD0e17KCqTYCKUs2trp5ZzT-pU339VK765IBO6U0zvWRI0u1aDEvFjKCqCMjONQrSME2h-PUa_slvsapO8joCiUuTGERJ4uE38eTmoeSfG3oxdxrltL3NJtX5eMZt2Y9TgFEbcznTOYeVDWpvd5f197W0JX0GONxLzQAmoE3dTzrhEbGJXa7VT4LKYbeGrnm5RlbLU6kG8o6GERTzhdaWp1rkM8sQJE0TqsHA/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2Frel7downloads__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx

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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<mailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edu<mailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edumailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto:XNA@uams.edu%3cmailto: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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1rt1YtfHh4XlSiwG68TcMJ91IR09LVfLg8tsZVDwlipbmKq...<https://secure-web.cisco.com/1bNGpGOTAND8Wq1UdbAnSnxAQdb_fRCU_9aKUuYtaaaldMo...<https://secure-web.cisco.com/1gw19JJdXeeyzHmzwhtTu2vnf0uClwX3yJXKZ1YQi3DQqBb...https://secure-web.cisco.com/1el5uOumhLMir_zrAWFEgOCkfd_60AK_ewQEr7S4c5ii30TYQnv-x-yoY2wR6-0VYY-F9TxKy6dlRv-lgHzHbovWRW7MTdvuuPEP5Ep4HhkobzWx2ntumME6OxEGpqxh6Kbr_sesgnZHE0LwvWix2OeSy4MMyoVfPICQlqENhuAlorvliz8urSt0wdYdarxQ22OxOfGt8Jaa-Lg7V0DPo9aj1SkBcCRQfAjnbypebPDe7laG4qB6LW4bHfXR9mDV3engrR84HkcqoFFxIer9WLqoM_q0Ak-CNVxBJjf2JIP3CxkV9ZcZGVs3KMhTW7Ur2DQdsYtO3ngYMj6I0qyW0xA/https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting__;!!LFqOYw!rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1OaUQzJNRPo049e0G3gE7Svl2Z8-MWvMQ6O-8qzfk_20N7GLezlIKD7mW0K1Ee7_c_6_2zewxx7Iib8Knm_tTL-cwpOHfT5qvJpf6mdcuxX03P9uRuE0s-bZ3b3fBVSVbsf6nqSmmLShMDwtuliQ3EwTiON8GQMaC0ZKvHvkTjFXe4IFB_-2pMbktHuXm1MQQzrjpyu57CSZ_5u9tF8A9NRO47FkqmqYqwZo-DOyb0w5MeElRYx2c6By4DouUz8gziaDzP-eD4PbkttUmev26M3JGIRa1iTd82WeCZHoUh5z3TyDK0EkffTZjxw4YHz84OSP-IHY0DMYXF7QxBb49qw/https*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FBugReporting__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA*24__;JSUlJSUlJSUlJSUlJSU!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaN-J8pIDQ$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1XQCbKYk8dPlPndcc-CWngT1LMlXOkav_qc5WZkzwS1_W8nGf1ewc1odzRecVmXVbCdTtHWBWPEhTynwSihjw9zIm9vI7_ok39sPyY25kL8ZcrKLGKefqQhcFcZ7jRb6UHQ58824zswlD6khQ-wIoBG_s8Vn1tNNlWg1D8tu81SiOGE9ehQuikt3h74iAKqnusd1GyLWfrlkvVo2Qrut1qCWDPfvIIVv4-Dx2fx78k3rSdqeE2wG-M-9Z5Hh7cCx0b0FEyD4JPcRtY_pnDB-KJFJ6_TGMlKBxOUSHXQRkfUt1JjL-YhvfIKrL5VlxvDdL/https*3A*2F*2Furldefense.com*2Fv3*2F__http*3A*2Fsurfer.nmr.mgh.harvard.edu*2Ffswiki*2FBugReporting__*3B*21*21LFqOYw*21rrxnktSjJS824qT0_NjEZpDZY1PFMdQ_XCwaFRFQmc_4xCo8b2HzfDeRGuUSHdQ3RYdx9vRxPCzswNR18aKWGA*24*253chttps*3A*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1OaUQzJNRPo049e0G3gE7Svl2Z8-MWvMQ6O-8qzfk_20N7GLezlIKD7mW0K1Ee7_c_6_2zewxx7Iib8Knm_tTL-cwpOHfT5qvJpf6mdcuxX03P9uRuE0s-bZ3b3fBVSVbsf6nqSmmLShMDwtuliQ3EwTiON8GQMaC0ZKvHvkTjFXe4IFB_-2pMbktHuXm1MQQzrjpyu57CSZ__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJQ!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMp1xOZ-wQ$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1Trtx7sidR3RBuLtO_V__UW62fB-2m0kP9x8DQyEE0eBMQwcQI7mzS3ScR2UKvpVFESfcXgy2uoF28DkjM-IXa6SUTWHCyXEmAe0GVgWYB8fbgz8hwEsQ3yQt6yY7

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Regards,

Xiaoxu

________________________________

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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1CfNI9TlTSe619krrdTn_-TZDpmeFXQcG99RScdgc8t6i5S...<https://secure-web.cisco.com/1dJt5pXhtrs-iJz1sRL0kmH2yxJuvhukmMbx9-R97Sjg__h...<https://secure-web.cisco.com/1ZjomqzLJVULfBCtQ8P4J11pFAhJjTtjI0dayRn5uBoJYTk...https://secure-web.cisco.com/1HHw_JTdsMiaHpoGzuURqWgwnp5HVnYRlXNo93hw11YqTjkgJu0stvj2r35u3QbGO7LhxuV6NsA8jtQ4DS21piPCWjvoKJZpM8CL4NowWvfjFX9A5QBTAmP-5AdrXRpo8TNmQitIOrStMV9x6NAsYGwHrAxOjKEBxzDRHwk9iNUZWhRAYU3HOOhCPmKBWOtFGggHQzcSyDErRwO-StNdhyqv5o5UjZZ7adg7uFMyyqX4DqbcGHj3YPBLeQgtbAiZGjcIbVdmgly3S2PV0QAIu9rCXa8QgfCnciIkSwy0ajCeEjjffyS5nMnCgnzYSfZHfUwMgeVBIgfciH8mRCpxvDA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaM7YzvDaA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1TIdBmFypCkFt802rAmLuVMS5u9x8k_ivwKbx2BmowQz-JRiWjctMyh7uRg1rYxTW28Nvj94Qh5FHA-UeDKaSEtkpKTqj-VixZ-FWhgy-EE-qN3M2LiNejsC-nvYnwLpAp4Nkt3IlWpgPL9iWMKlE2MZZXcHQfHuS4dFp86P3I3dAOJvZhzt2lFZMivS2skN-x2soLwz9ozVCLZjpA8V_T8LD7ZWEGcuWk6ri0AD-Kq0TbCRhimb_4i0s0sSxtbJUTeJXDE5Deq7SarpDRXS50xGdVhRTwdsxMOP-OzF7FyXwJ7CkdiT5vqh6EBkCKaOj/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__*3B*21*21LFqOYw*21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaM7YzvDaA*24__;JSUlJSUlJSUlJSUlJSUl!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMpfxkfAbw$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1AaSVF37t5YJfXze062pNgrLWHrzj1kHDhCDTtz7AulpmEdAj_mI9gSG2Gd47G4b76pYsTg4kkERAPO8LeBwRteDZjAcGtmbO57i67Nd9zl-JYrqnO07xRIvrNkSU2W5zBWRvgN0n7VDeRJb7VcPdAwf2j_73mkJKxCtzvUBxjMMSDN_YEyW3w2I_S6RxLh89M_UE8ibKtadXs5Id7klzwxI4z9PI94s9ayfXxO-41mFaghq6a8XSFFLgYUJgfjfVCogRR9ODlVMT4aBAFQJq8xPLADb0ShbBKThPXn9aldDvoJMBN_2EaGxgFYmdYRhX/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__*3B*21*21LFqOYw*21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaM7YzvDaA*24*253chttps*3A*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1TIdBmFypCkFt802rAmLuVMS5u9x8k_ivwKbx2BmowQz-JRiWjctMyh7uRg1rYxTW28Nvj94Qh5FHA-UeDKaSEtkpKTqj-VixZ-FWhgy-EE-qN3M2LiNejsC-nvYnwLpAp4Nkt3IlWpgPL9iWMKlE2MZZXcHQfHuS4dFp86P3I3dAOJvZhzt2lFZMivS2skN-x2soLwz9ozVCLZjpA8V_T8LD7ZWEGcuWk6ri0AD-Kq0TbCRhimb_4i0s0sSxtbJUTeJXDE5Deq7SarpDRXS50xGdVhRTwdsxMOP-OzF7FyXwJ7CkdiT5vqh6EBkCK__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSU!!LFqOYw!rJFAzZ4pXQ79Dmu5mIEef8olXY__W0USXDul-P8YbOdN3Gy4MGbG934CwKf4Ha6W_i1WFMbMj1eklrxbdZrB5A$

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZsLICgid4qSicr5CpnNoP0g2IBeM892RM0vCTClaYT9JIu...<https://secure-web.cisco.com/1nuFtj1bRPP7-fJ17mXhRk3cpzsMo3sxFk7i4tGax7uXbd6...<https://secure-web.cisco.com/1Nk5NDrEbpyUlJvEpo6D5U_A9TlM_g7zNVPunkAwuPvItuL...https://secure-web.cisco.com/1N1RDnfcorlH0Q40bBHjtz44x7KdLwH7p8LqR5BLDG4KxJrtueok-v8BrR3uQjUOToMOK7UT68cj3ad01pmMAnPGVYyBtmMtO9SzVJhb3JmpzBslE5kdOeCNyuc5YWr1DFcZC1dAaN18oRx5mFISCbjIo16A9BnmPKQuTe3-ByE80ZIis_8NJCozqy11SUja8NZWb38ZL3x2cZnUO0ZhnCTgFVotWFOHYyFWJqEkvSWcEnU49LNJHg6KAHbmpLS6qx4Ux0hJ_x5arYhJpQ-FlV-uWyVJVh6EQ-bldJGUZvjA2Qv5bncU0UhfW_MeeMJ6O9Qyrvlo1A3dWIhw26squDw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fwww.massgeneralbrigham.org%2Fcomplianceline__;!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMt35Bu4g$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1s20q8RUR2XuMW37F2RBYPmcaMrcR0pzOG3DzSrWtcrfrn5B4M37p-9nEUbOAAiaRfzqLht-M20lXYlfuq4MJvQWAQ_FQZgFdshvQqAMzOPK1uheq0J-NcEKDBYmF-zS9gvMfVRm5KR0xKTv8jHAenWpKU5XND8W_LpAW669X3lY-86JUakDtM0hx2k2gYEwOrl8-6eW8N89Qaya5miOKkynKxHQo6jh1PhUWo1_SIQ3uTVQSjsu6Hi_Avi7na3OtYopttDGclJrwSLCKCcL3NDX4AE8zP3k-Xqql2R4B3EWXCDkdxsgl81m2S-QjD2N0/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fwww.massgeneralbrigham.org*2Fcomplianceline__*3B*21*21LFqOYw*21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMt35Bu4g*24__;JSUlJSUlJSUlJSUlJQ!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMrHhbxcfQ$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1nQqAYNZGnzJY8FYUhrxj-qNdLonr4FXS3WkKkdaGCp2gucD3FtL-NgXQNtCnLGeYFBhYMF3vpJ6GkPbAoRNBCuvjvGI-Pj4xFF4ZfK8O_PYbxTlrct4EPh-968YtE7uwvU1nudSjO0e4JekXWe3qj0P6yKInCVhp_w04wVD57kB7vv_FsI6G17-G8iCPpYwXS5kQ_Fs13_Z5n3ZgDn0vqU1512irCTEpYMGNLl_eIy6fxYlmDZVnbTSkaNbK1U845cFIaM1vmvH5U3tOvT8eWnF-8SIAaJhB2BIo0WL7C3A5l3X1j-s4kULME_nUhNwA/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fwww.massgeneralbrigham.org*2Fcomplianceline__*3B*21*21LFqOYw*21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMt35Bu4g*24*253chttps*3A*2Furldefense.com*2Fv3*2F__https*3A*2Fsecure-web.cisco.com*2F1s20q8RUR2XuMW37F2RBYPmcaMrcR0pzOG3DzSrWtcrfrn5B4M37p-9nEUbOAAiaRfzqLht-M20lXYlfuq4MJvQWAQ_FQZgFdshvQqAMzOPK1uhe__;JSUlJSUlJSUlJSUlJSUlJSUlJSUl!!LFqOYw!rJFAzZ4pXQ79Dmu5mIEef8olXY__W0USXDul-P8YbOdN3Gy4MGbG934CwKf4Ha6W_i1WFMbMj1eklrwSCOoziw$

q0J-NcEKDBYmF-zS9gvMfVRm5KR0xKTv8jHAenWpKU5XND8W_LpAW669X3lY-86JUakDtM0hx2k2gYEwOrl8-6eW8N89Qaya5miOKkynKxHQo6jh1PhUWo1_SIQ3uTVQSjsu6Hi_Avi7na3OtYopttDGclJrwSLCKCcL3NDX4AE8zP3k-Xqql2R4B3EWXCDkdxsgl81m2S-QjD2N0%2Fhttps%2A3A%2A2F%2A2Furldefense.com%2A2Fv3%2A2F__https%2A3A%2A2Fwww.massgeneralbrigham.org%2A2Fcomplianceline__%2A3B%2A21%2A21LFqOYw%2A21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMt35Bu4g%2A24__%3BJSUlJSUlJSUlJSUlJQ%21%21LFqOYw%21vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMrHhbxcfQ%24>> <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZsLICgid4qSicr5CpnNoP0g2IBeM892RM0vCTClaYT9JIu...<https://secure-web.cisco.com/1nuFtj1bRPP7-fJ17mXhRk3cpzsMo3sxFk7i4tGax7uXbd6...<https://secure-web.cisco.com/1Nk5NDrEbpyUlJvEpo6D5U_A9TlM_g7zNVPunkAwuPvItuL...https://secure-web.cisco.com/1N1RDnfcorlH0Q40bBHjtz44x7KdLwH7p8LqR5BLDG4KxJrtueok-v8BrR3uQjUOToMOK7UT68cj3ad01pmMAnPGVYyBtmMtO9SzVJhb3JmpzBslE5kdOeCNyuc5YWr1DFcZC1dAaN18oRx5mFISCbjIo16A9BnmPKQuTe3-ByE80ZIis_8NJCozqy11SUja8NZWb38ZL3x2cZnUO0ZhnCTgFVotWFOHYyFWJqEkvSWcEnU49LNJHg6KAHbmpLS6qx4Ux0hJ_x5arYhJpQ-FlV-uWyVJVh6EQ-bldJGUZvjA2Qv5bncU0UhfW_MeeMJ6O9Qyrvlo1A3dWIhw26squDw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fwww.massgeneralbrigham.org%2Fcomplianceline__;!!LFqOYw!oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMt35Bu4g$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1s20q8RUR2XuMW37F2RBYPmcaMrcR0pzOG3DzSrWtcrfrn5B4M37p-9nEUbOAAiaRfzqLht-M20lXYlfuq4MJvQWAQ_FQZgFdshvQqAMzOPK1uheq0J-NcEKDBYmF-zS9gvMfVRm5KR0xKTv8jHAenWpKU5XND8W_LpAW669X3lY-86JUakDtM0hx2k2gYEwOrl8-6eW8N89Qaya5miOKkynKxHQo6jh1PhUWo1_SIQ3uTVQSjsu6Hi_Avi7na3OtYopttDGclJrwSLCKCcL3NDX4AE8zP3k-Xqql2R4B3EWXCDkdxsgl81m2S-QjD2N0/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fwww.massgeneralbrigham.org*2Fcomplianceline__*3B*21*21LFqOYw*21oYl0pRI0vnOIbQmIxKc7WC-xezxwI76P7M3UL0tEO6NUZJXqSSPQsXRiRTNfmRh_gH_vrTjY2MjTCaMt35Bu4g*24__;JSUlJSUlJSUlJSUlJQ!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMrHhbxcfQ$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1nQqAYNZGnzJY8FYUhrxj-qNdLonr4FXS3WkKkdaGCp2gucD3FtL-NgXQNtCnLGeYFBhYMF3vpJ6GkPbAoRNBCuvjvGI-Pj4xFF4ZfK8O_PYbxTlrct4EPh-968YtE7uwvU1nudSjO0e4JekXWe3qj0P6yKInCVhp_w04wVD57kB7vv_FsI6G17-G8iCPpYwXS5kQ_Fs13_Z5n3ZgDn0vqU1512irCTEpYMGNLl_eIy6fxYlmDZVnbTSkaNbK1U845cFIaM1vmvH5U3tOvT8eWnF-8SIAaJhB2BIo0WL7C3A5l3X1j-s4kULME_nUhNwA/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fwww.massgeneralbr__;JSUlJSUlJQ!!LFqOYw!rJFAzZ4pXQ79Dmu5mIEef8olXY__W0USXDul-P8YbOdN3Gy4MGbG934CwKf4Ha6W_i1WFMbMj1eklrwKhq-nuQ$

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MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1CfNI9TlTSe619krrdTn_-TZDpmeFXQcG99RScdgc8t6i5S...<https://secure-web.cisco.com/1DE2gQr5zAFNhnpgszjmnXlQ-xu9jp0CGFvIJFCoqdGdIAZ...https://secure-web.cisco.com/1HHw_JTdsMiaHpoGzuURqWgwnp5HVnYRlXNo93hw11YqTjkgJu0stvj2r35u3QbGO7LhxuV6NsA8jtQ4DS21piPCWjvoKJZpM8CL4NowWvfjFX9A5QBTAmP-5AdrXRpo8TNmQitIOrStMV9x6NAsYGwHrAxOjKEBxzDRHwk9iNUZWhRAYU3HOOhCPmKBWOtFGggHQzcSyDErRwO-StNdhyqv5o5UjZZ7adg7uFMyyqX4DqbcGHj3YPBLeQgtbAiZGjcIbVdmgly3S2PV0QAIu9rCXa8QgfCnciIkSwy0ajCeEjjffyS5nMnCgnzYSfZHfUwMgeVBIgfciH8mRCpxvDA/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer__;!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMo3cd8dCQ$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1-3JaDhhl1YVx3OgxPNtIB4EmNjSkMAsMDPu46icX1ORwifYO6AvkOhTKcbnlB--QiMaXzA6Ns7BExHhDSSN30seZXexbIJNvty3FYFWsIROVyv-1mwmUA6V_Ek96zZQUnwzqz4D5ecVu2wTK6_BOx_PJjt-RKOCUYad_Jpyu0S5P4crpUdaBBNfGL6ke3ZI-_8o9m-cbp-8lahb-R405rCX3F3Xk1vMOg-ZkI4KGSPbnnUzkkof6jxpbQsCXev61-YJJck6vjQZwpo9NnxUgg4yqAMlR_x1azkg13WhuSE9TrwBnSMr8lhoqz_F_tonV/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fmail.nmr.mgh.harvard.edu*2Fmailman*2Flistinfo*2Ffreesurfer__*3B*21*21LFqOYw*21vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMo3cd8dCQ*24__;JSUlJSUlJSUlJSUlJSUl!!LFqOYw!rJFAzZ4pXQ79Dmu5mIEef8olXY__W0USXDul-P8YbOdN3Gy4MGbG934CwKf4Ha6W_i1WFMbMj1eklrwCICa3zw$>

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZsLICgid4qSicr5CpnNoP0g2IBeM892RM0vCTClaYT9JIu...<https://secure-web.cisco.com/1BSw25f8IfDa_MriCh0Gg6Ewx9hyVm3NiJ1MyHxyg94qyS1...https://secure-web.cisco.com/1N1RDnfcorlH0Q40bBHjtz44x7KdLwH7p8LqR5BLDG4KxJrtueok-v8BrR3uQjUOToMOK7UT68cj3ad01pmMAnPGVYyBtmMtO9SzVJhb3JmpzBslE5kdOeCNyuc5YWr1DFcZC1dAaN18oRx5mFISCbjIo16A9BnmPKQuTe3-ByE80ZIis_8NJCozqy11SUja8NZWb38ZL3x2cZnUO0ZhnCTgFVotWFOHYyFWJqEkvSWcEnU49LNJHg6KAHbmpLS6qx4Ux0hJ_x5arYhJpQ-FlV-uWyVJVh6EQ-bldJGUZvjA2Qv5bncU0UhfW_MeeMJ6O9Qyrvlo1A3dWIhw26squDw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fwww.massgeneralbrigham.org%2Fcomplianceline__;!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMoIdosxiA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1irSPWSVjORbJSdeQBUEjIqHz_bgBmaNpj4eY9X6X_16JGMYYoOU3CN-0jw9MvJeiZsUx4CO0cQ68qsuDsS3A75wGTj0mbUpuYw6cVbSAoYRmHdf0GrqrJDjjOGtZj7n4wYZKXOpChspzfmMHoteoyTZH41FWXc0jy3HkTPgN8LaKgPv0VrVofjrKpuPI93cDpFAS6m75x6uwpIpPLxX6tNglqbOD4HwjY_3zmZwG2PQYQYfDJ8kRozWVusgbTpHbhXjjq5jdZmZn3aq7W3b8vFPwGEl22t4tV-DN2uHV0thhSNoMzGziSqjtegecPago/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fwww.massgeneralbrigham.org*2Fcomplianceline__*3B*21*21LFqOYw*21vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMoIdosxiA*24__;JSUlJSUlJSUlJSUlJQ!!LFqOYw!rJFAzZ4pXQ79Dmu5mIEef8olXY__W0USXDul-P8YbOdN3Gy4MGbG934CwKf4Ha6W_i1WFMbMj1eklryjSJKHxg$> <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1ZsLICgid4qSicr5CpnNoP0g2IBeM892RM0vCTClaYT9JIu...<https://secure-web.cisco.com/1BSw25f8IfDa_MriCh0Gg6Ewx9hyVm3NiJ1MyHxyg94qyS1...https://secure-web.cisco.com/1N1RDnfcorlH0Q40bBHjtz44x7KdLwH7p8LqR5BLDG4KxJrtueok-v8BrR3uQjUOToMOK7UT68cj3ad01pmMAnPGVYyBtmMtO9SzVJhb3JmpzBslE5kdOeCNyuc5YWr1DFcZC1dAaN18oRx5mFISCbjIo16A9BnmPKQuTe3-ByE80ZIis_8NJCozqy11SUja8NZWb38ZL3x2cZnUO0ZhnCTgFVotWFOHYyFWJqEkvSWcEnU49LNJHg6KAHbmpLS6qx4Ux0hJ_x5arYhJpQ-FlV-uWyVJVh6EQ-bldJGUZvjA2Qv5bncU0UhfW_MeeMJ6O9Qyrvlo1A3dWIhw26squDw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fwww.massgeneralbrigham.org%2Fcomplianceline__;!!LFqOYw!vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMoIdosxiA$%3chttps:/urldefense.com/v3/__https:/secure-web.cisco.com/1irSPWSVjORbJSdeQBUEjIqHz_bgBmaNpj4eY9X6X_16JGMYYoOU3CN-0jw9MvJeiZsUx4CO0cQ68qsuDsS3A75wGTj0mbUpuYw6cVbSAoYRmHdf0GrqrJDjjOGtZj7n4wYZKXOpChspzfmMHoteoyTZH41FWXc0jy3HkTPgN8LaKgPv0VrVofjrKpuPI93cDpFAS6m75x6uwpIpPLxX6tNglqbOD4HwjY_3zmZwG2PQYQYfDJ8kRozWVusgbTpHbhXjjq5jdZmZn3aq7W3b8vFPwGEl22t4tV-DN2uHV0thhSNoMzGziSqjtegecPago/https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2Fwww.massgeneralbrigham.org*2Fcomplianceline__*3B*21*21LFqOYw*21vWT5kAH_0TvjGeDa0AT9mvvwvZ1PccCxQW97akyiemKYshYIgkCH6NhyAkuhzW0M1jnIQvuMqLWxaMoIdosxiA*24__;JSUlJSUlJSUlJSUlJQ!!LFqOYw!rJFAzZ4pXQ79Dmu5mIEef8olXY__W0USXDul-P8YbOdN3Gy4MGbG934CwKf4Ha6W_i1WFMbMj1eklryjSJKHxg$>> .

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Freesurfer@nmr.mgh.harvard.edu

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1ZsLICgid4qSicr5CpnNoP0g2IBeM892RM0vCTClaYT9JIu...https://secure-web.cisco.com/1N1RDnfcorlH0Q40bBHjtz44x7KdLwH7p8LqR5BLDG4KxJrtueok-v8BrR3uQjUOToMOK7UT68cj3ad01pmMAnPGVYyBtmMtO9SzVJhb3JmpzBslE5kdOeCNyuc5YWr1DFcZC1dAaN18oRx5mFISCbjIo16A9BnmPKQuTe3-ByE80ZIis_8NJCozqy11SUja8NZWb38ZL3x2cZnUO0ZhnCTgFVotWFOHYyFWJqEkvSWcEnU49LNJHg6KAHbmpLS6qx4Ux0hJ_x5arYhJpQ-FlV-uWyVJVh6EQ-bldJGUZvjA2Qv5bncU0UhfW_MeeMJ6O9Qyrvlo1A3dWIhw26squDw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fwww.massgeneralbrigham.org%2Fcomplianceline__;!!LFqOYw!rJFAzZ4pXQ79Dmu5mIEef8olXY__W0USXDul-P8YbOdN3Gy4MGbG934CwKf4Ha6W_i1WFMbMj1eklrypxtT16A$ <https://secure-web.cisco.com/1ZsLICgid4qSicr5CpnNoP0g2IBeM892RM0vCTClaYT9JIu...https://secure-web.cisco.com/1N1RDnfcorlH0Q40bBHjtz44x7KdLwH7p8LqR5BLDG4KxJrtueok-v8BrR3uQjUOToMOK7UT68cj3ad01pmMAnPGVYyBtmMtO9SzVJhb3JmpzBslE5kdOeCNyuc5YWr1DFcZC1dAaN18oRx5mFISCbjIo16A9BnmPKQuTe3-ByE80ZIis_8NJCozqy11SUja8NZWb38ZL3x2cZnUO0ZhnCTgFVotWFOHYyFWJqEkvSWcEnU49LNJHg6KAHbmpLS6qx4Ux0hJ_x5arYhJpQ-FlV-uWyVJVh6EQ-bldJGUZvjA2Qv5bncU0UhfW_MeeMJ6O9Qyrvlo1A3dWIhw26squDw/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fwww.massgeneralbrigham.org%2Fcomplianceline__;!!LFqOYw!rJFAzZ4pXQ79Dmu5mIEef8olXY__W0USXDul-P8YbOdN3Gy4MGbG934CwKf4Ha6W_i1WFMbMj1eklrypxtT16A$> .

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