The 'matlab runtime' (MCR) installed by fs_install_mcr lets you run compiled
matlab binaries, but it’s different from having matlab actually installed on
your system. MCR is used to run the sub-structure segmentation tools, but
mris_compute_lgi is a command that runs matlab scripts directly, so it’s
required that you have matlab installed on your computer to use it.
best
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Georgia Kapizioni
<geo.kapizi...@gmail.com>
Date: Wednesday, March 10, 2021 at 6:35 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Matlab version 2012b installation problem
External Email - Use Caution
Hello Andrew,
Thank you once again for your help and apologies for writing one more time, but
it seems that Freesurfer cannot detect/recognise Matlab. When I tried to ran
local gyrification index for one participant, I got the following error:
recon-all -s HD01 -localGI
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Users/georgina/Downloads/HDf
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r-- 1 georgina staff 1188013 Mar 10 13:20
/Users/georgina/Downloads/HDf/HD01/scripts/recon-all.log
Darwin Georgias-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug
31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64
/Users/georgina/Downloads/HDf/HD01/surf
#--------------------------------------------
#@# Local Gyrification Index lh Wed Mar 10 13:24:00 EET 2021
\n mris_compute_lgi --i lh.pial \n
ERROR: Matlab is required to run mris_compute_lgi!
Darwin Georgias-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug
31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64
recon-all -s HD01 exited with ERRORS at Wed Mar 10 13:24:00 EET 2021
Attached please also find the recon-all.error.
When I go to Freesurfer directory and type: ls -l
$FREESURFER_HOME/bin/fs_install_mcr
The output is: -rw-r--r-- 1 root wheel 2010 Mar 6 12:03
/Applications/freesurfer/bin/fs_install_mcr
Do you have any idea about what went wrong?
Thank you once more time.
Best,
Georgia
On 1 Mar 2021, at 5:57 PM, Georgia Kapizioni
<geo.kapizi...@gmail.com<mailto:geo.kapizi...@gmail.com>> wrote:
Hello Andrew,
Thank you so much for your response.
Here is the output when running the command you suggested:
Georgias-MacBook-Pro:~ georgina$ curl MailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" claiming to be
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr<https://secure-web.cisco.com/185rmofowsgEkR6fz3yHPDaV0Tlx75MQaLUX8iyP1fVjojzFqQSDrXIKGx2JM1Mk13YhPqwuUD1LvXNaQhwaH2d8L1z4bcK8yOkSgXfPM9uga4RT38vj7uRBTt9maIn86ZzeYpWTPEiG7aaNEGM-PmPdsE4O1KxuKlbu6zFXZ9k76NkLo65H0yHUmbdnu77Tfvy3B6TuvD63EwEg8Sk6IYSqeuba1CeFlOPLnfH0IuxgYQIAHZ1118Ym3e6YUh-5ZzC7PSlQPF6FLzudRa40mcQ/https%3A%2F%2Fraw.githubusercontent.com%2Ffreesurfer%2Ffreesurfer%2Fdev%2Fscripts%2Ffs_install_mcr>
-o fs_install_mcr
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 2010 100 2010 0 0 8170 0 --:--:-- --:--:-- --:--:-- 8137
(base) Georgias-MacBook-Pro:~ georgina$ ls fs_install_mcr
fs_install_mcr
I assume, it didn’t download it, right?
Georgia
On 26 Feb 2021, at 8:03 PM, Georgia Kapizioni
<geo.kapizi...@gmail.com<mailto:geo.kapizi...@gmail.com>> wrote:
Hello Andrew,
Please accept my apologies for such a detailed response, I had a health issue,
and I was just able to test what you suggested.
When I use the wget command, again I have an error: -bash: wget: command not
found
Any ideas on how to overcome this issue?
Thank you once again,
Best,
Georgia
On 9 Feb 2021, at 5:49 PM, Georgia Kapizioni
<geo.kapizi...@gmail.com<mailto:geo.kapizi...@gmail.com>> wrote:
Hello Andrew,
Thank you for your response!
The output of the first command (meaning sudo cd $FREESURFER_HOME/bin && curl
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
claiming to be
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr<https://secure-web.cisco.com/185rmofowsgEkR6fz3yHPDaV0Tlx75MQaLUX8iyP1fVjojzFqQSDrXIKGx2JM1Mk13YhPqwuUD1LvXNaQhwaH2d8L1z4bcK8yOkSgXfPM9uga4RT38vj7uRBTt9maIn86ZzeYpWTPEiG7aaNEGM-PmPdsE4O1KxuKlbu6zFXZ9k76NkLo65H0yHUmbdnu77Tfvy3B6TuvD63EwEg8Sk6IYSqeuba1CeFlOPLnfH0IuxgYQIAHZ1118Ym3e6YUh-5ZzC7PSlQPF6FLzudRa40mcQ/https%3A%2F%2Fraw.githubusercontent.com%2Ffreesurfer%2Ffreesurfer%2Fdev%2Fscripts%2Ffs_install_mcr>
-o fs_install_mcr && chmod +x) was:
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 2010 100 2010 0 0 5275 0 --:--:-- --:--:-- --:--:-- 5261
usage: chmod [-fhv] [-R [-H | -L | -P]] [-a | +a | =a [i][# [ n]]] mode|entry
file ...
chmod [-fhv] [-R [-H | -L | -P]] [-E | -C | -N | -i | -I] file …
However, when I type: ls -l $FREESURFER_HOME/bin/fs_install_mcr as you
suggested, it appears ls: /Applications/freesurfer/bin/fs_install_mcr: No such
file or directory
When I type again fs_install_mcr while being in Freesurfer/bin path again
fs_install_mcr: command not found appears.
Any idea what went wrong?
Thanks once again,
Best,
Georgia
On 9 Feb 2021, at 1:05 AM, Georgia Kapizioni
<geo.kapizi...@gmail.com<mailto:geo.kapizi...@gmail.com>> wrote:
Dear Freesurfer experts,
I am trying to install Matlab version 2012b but a message appears: command not
found.
Firstly, I ran: sudo cd $FREESURFER_HOME/bin && curl MailScanner has detected a
possible fraud attempt from "secure-web.cisco.com" claiming to be
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr<https://secure-web.cisco.com/185rmofowsgEkR6fz3yHPDaV0Tlx75MQaLUX8iyP1fVjojzFqQSDrXIKGx2JM1Mk13YhPqwuUD1LvXNaQhwaH2d8L1z4bcK8yOkSgXfPM9uga4RT38vj7uRBTt9maIn86ZzeYpWTPEiG7aaNEGM-PmPdsE4O1KxuKlbu6zFXZ9k76NkLo65H0yHUmbdnu77Tfvy3B6TuvD63EwEg8Sk6IYSqeuba1CeFlOPLnfH0IuxgYQIAHZ1118Ym3e6YUh-5ZzC7PSlQPF6FLzudRa40mcQ/https%3A%2F%2Fraw.githubusercontent.com%2Ffreesurfer%2Ffreesurfer%2Fdev%2Fscripts%2Ffs_install_mcr>
-o fs_install_mcr && chmod +x
Then I typed: fs_install_mcr R2012b and I receive: command not found.
My FS version is 6 and I have already install Matlab2016_b on my Mac.
Could you please help me resolve this issue?
Thank you in advance,
Georgia
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