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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Georgia Kapizioni <geo.kapizioni@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.kapizioni@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 -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.kapizioni@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.kapizioni@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 -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.kapizioni@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 -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