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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 $FREESURFER_HOME/bin/fs_install_mcr The output is: -rw-r--r-- 1 root wheel 2010 Mar 6 12:03 /Applications/freesurfer/bin/fs_install_mcr
Do you have any idea about what went wrong? Thank you once more time. Best, Georgia
On 1 Mar 2021, at 5:57 PM, Georgia Kapizioni geo.kapizioni@gmail.com wrote:
Hello Andrew,
Thank you so much for your response.
Here is the output when running the command you suggested:
Georgias-MacBook-Pro:~ georgina$ curl https://secure-web.cisco.com/185rmofowsgEkR6fz3yHPDaV0Tlx75MQaLUX8iyP1fVjojz... 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.kapizioni@gmail.com mailto: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 mailto: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 https://secure-web.cisco.com/185rmofowsgEkR6fz3yHPDaV0Tlx75MQaLUX8iyP1fVjojz... 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.kapizioni@gmail.com mailto: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 https://secure-web.cisco.com/185rmofowsgEkR6fz3yHPDaV0Tlx75MQaLUX8iyP1fVjojz... 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