Re: [Freesurfer] Matlab version 2012b installation problem

Wed, 10 Mar 2021 03:36:00 -0800

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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

Attachment: recon-all.error
Description: Binary data


On 1 Mar 2021, at 5:57 PM, Georgia Kapizioni <geo.kapizi...@gmail.com> wrote:

Hello Andrew,

Thank you so much for your response.

Here is the output when running the command you suggested:

  % 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> 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> wrote:

Hello Andrew,

Thank you for your response!

 % 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> wrote:

Dear Freesurfer experts, 

I am trying to install Matlab version 2012b but a message appears: command not found. 

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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