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