External Email - Use Caution
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/1aj9gsBgtgn7YY-Cjp-4RTDQ9ZZ-zSt6U2uLhCNs0DAt-2N... -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
Hi Georgia,
If you downloaded the runtime installer script to FREESURFER_HOME, which it looks like you did, the command should be available to run as long as you’ve also sourced that version of freesurfer, i.e. $FREESURFER_HOME/bin is in your PATH.
If this is the case and it still can’t find the command, you should make sure it actually downloaded correctly. Did the initial command finish with errors? And what’s the output of running:
ls -l $FREESURFER_HOME/bin/fs_install_mcr
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: Monday, February 8, 2021 at 6:06 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Matlab version 2012b installation problem
External Email - Use Caution 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_insta...https://secure-web.cisco.com/1aj9gsBgtgn7YY-Cjp-4RTDQ9ZZ-zSt6U2uLhCNs0DAt-2NTByXvzSozOvPPBzayeJeLvAT5irVaUjy4aLBMhakn_GAeAmj3xCDf6LD8yJ6sh9CKRMGK62ILhguuZGZ_8bB4I-aI33wlezoPHr9dAWn7IzPvaTnGQHfSnlfKzU8bqP_aePH6KSeoBS33CO5XUWoIPGbpWg-9AQRNzYc__WWNS-u406NNKMS1PqVr0eeF9Glneb8Q7XYckiL3ZeYmkRD7-gySx_Hdw34dXvLorjw/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
External Email - Use Caution
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/192SY1imdcuc4zr9u8lZ1JV_1CRED5vMVWM-4sp-sXHUpJ3... -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 https://secure-web.cisco.com/192SY1imdcuc4zr9u8lZ1JV_1CRED5vMVWM-4sp-sXHUpJ3... https://secure-web.cisco.com/192SY1imdcuc4zr9u8lZ1JV_1CRED5vMVWM-4sp-sXHUpJ31aPv2mpOW0dWjJePYjrWVeofQbxrp0l9y6250pwGYIlKsUyxCMSJdghxpFapabMDgioD_lO70Ttn9jPzrNJWks7zMExZreQJPZzhVtRjJU4_LT9TfyP192WPJ9jRgQfgGwiWALmDneJwfSqg4CAlfFkqbqzL6Iocd-zXAqWzyHEu39_iFVnzO5J2Evmrtn0ivSqZNnVSsPuLFOCw9CYZQ6uteF5AWm0kJdz_6XXg/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
Hi Georgia,
I think you forgot to run the last word "fs_install_mcr" in that command (after chmod +x). That’s why chmod is throwing a usage error. That doesn’t solve the reason why it’s not downloading though. Can you try a different tool, like wget and let me know if anything downloaded:
wget https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_insta...
Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Georgia Kapizioni geo.kapizioni@gmail.com Date: Tuesday, February 9, 2021 at 10:49 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 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_insta...https://secure-web.cisco.com/192SY1imdcuc4zr9u8lZ1JV_1CRED5vMVWM-4sp-sXHUpJ31aPv2mpOW0dWjJePYjrWVeofQbxrp0l9y6250pwGYIlKsUyxCMSJdghxpFapabMDgioD_lO70Ttn9jPzrNJWks7zMExZreQJPZzhVtRjJU4_LT9TfyP192WPJ9jRgQfgGwiWALmDneJwfSqg4CAlfFkqbqzL6Iocd-zXAqWzyHEu39_iFVnzO5J2Evmrtn0ivSqZNnVSsPuLFOCw9CYZQ6uteF5AWm0kJdz_6XXg/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.commailto: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_insta...https://secure-web.cisco.com/192SY1imdcuc4zr9u8lZ1JV_1CRED5vMVWM-4sp-sXHUpJ31aPv2mpOW0dWjJePYjrWVeofQbxrp0l9y6250pwGYIlKsUyxCMSJdghxpFapabMDgioD_lO70Ttn9jPzrNJWks7zMExZreQJPZzhVtRjJU4_LT9TfyP192WPJ9jRgQfgGwiWALmDneJwfSqg4CAlfFkqbqzL6Iocd-zXAqWzyHEu39_iFVnzO5J2Evmrtn0ivSqZNnVSsPuLFOCw9CYZQ6uteF5AWm0kJdz_6XXg/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
External Email - Use Caution
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 https://secure-web.cisco.com/1bHtpwdS5JAjnUx-R0jitQWY7Cgew5buI-cT6yGrYhYQAYO... https://secure-web.cisco.com/1bHtpwdS5JAjnUx-R0jitQWY7Cgew5buI-cT6yGrYhYQAYOWA_rt6ItYwt9HvAY3xDLpmSnF0adfN_5oigED5GzMXZaEK8kXtTqy9jcdc2LVQwzReMBuNFh-j3EHpbRQrd5yGI8eLScEd-j8DT1LvYyeG9xFYTgAYo-7vJX2LQwSi-mX9Ja-n-8u6qTDUnNG97Y0OG58GPuqF-yjG0RdOwjGypCQLUVEVWUqGbQeRwYJ7zuVHDuqHabHo-JEIWKJQ/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/1bHtpwdS5JAjnUx-R0jitQWY7Cgew5buI-cT6yGrYhYQAYO... https://secure-web.cisco.com/1bHtpwdS5JAjnUx-R0jitQWY7Cgew5buI-cT6yGrYhYQAYOWA_rt6ItYwt9HvAY3xDLpmSnF0adfN_5oigED5GzMXZaEK8kXtTqy9jcdc2LVQwzReMBuNFh-j3EHpbRQrd5yGI8eLScEd-j8DT1LvYyeG9xFYTgAYo-7vJX2LQwSi-mX9Ja-n-8u6qTDUnNG97Y0OG58GPuqF-yjG0RdOwjGypCQLUVEVWUqGbQeRwYJ7zuVHDuqHabHo-JEIWKJQ/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
Hi Georgia,
No worries. It just means you’re missing wget, but we should probably figure out the problem with curl. From any directory, can you run:
curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_insta... -o fs_install_mcr ls fs_install_mcr
What’s the output of that?
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: Friday, February 26, 2021 at 1:04 PM 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,
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.commailto: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_insta...https://secure-web.cisco.com/1bHtpwdS5JAjnUx-R0jitQWY7Cgew5buI-cT6yGrYhYQAYOWA_rt6ItYwt9HvAY3xDLpmSnF0adfN_5oigED5GzMXZaEK8kXtTqy9jcdc2LVQwzReMBuNFh-j3EHpbRQrd5yGI8eLScEd-j8DT1LvYyeG9xFYTgAYo-7vJX2LQwSi-mX9Ja-n-8u6qTDUnNG97Y0OG58GPuqF-yjG0RdOwjGypCQLUVEVWUqGbQeRwYJ7zuVHDuqHabHo-JEIWKJQ/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.commailto: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 $FREESURFER_HOME/bin && curl MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_insta...https://secure-web.cisco.com/1bHtpwdS5JAjnUx-R0jitQWY7Cgew5buI-cT6yGrYhYQAYOWA_rt6ItYwt9HvAY3xDLpmSnF0adfN_5oigED5GzMXZaEK8kXtTqy9jcdc2LVQwzReMBuNFh-j3EHpbRQrd5yGI8eLScEd-j8DT1LvYyeG9xFYTgAYo-7vJX2LQwSi-mX9Ja-n-8u6qTDUnNG97Y0OG58GPuqF-yjG0RdOwjGypCQLUVEVWUqGbQeRwYJ7zuVHDuqHabHo-JEIWKJQ/https%3A%2F%2Fraw.githubusercontent.com%2Ffreesurfer%2Ffreesurfer%2Fdev%2Fscripts%2Ffs_install_mcr -o fs_install_mcr && chmod +x Then I typed: fs_install_mcr R2012b and I receive: command not found. My FS version is 6 and I have already install Matlab2016_b on my Mac.
Could you please help me resolve this issue? Thank you in advance, Georgia
External Email - Use Caution
Hello Andrew,
Thank you so much for your response.
Here is the output when running the command you suggested:
Georgias-MacBook-Pro:~ georgina$ curl https://secure-web.cisco.com/1tfNVXVQ3esQw4FySP0kMQiPkBCD_Bd9dwP_rQWbOUSswz4... -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 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/1tfNVXVQ3esQw4FySP0kMQiPkBCD_Bd9dwP_rQWbOUSswz4... https://secure-web.cisco.com/1tfNVXVQ3esQw4FySP0kMQiPkBCD_Bd9dwP_rQWbOUSswz4cGOB2TzCmn_v71kFHYK2FEvyKKrZDqwwL_IpLj5LrOyzhzZatukIqXUie48O8Jld4ys_JhH-PYptJ9v1_Uin1jZ4bmMVkbtCjJWYpaooz4qrfWAO_0_S826ay8Cudv7BTfD_1PEPWASGtfSCl5PRhw8IhZV98qdiD7p6saE4cGoDkWYYI311d1UaJasC1KVZYxrrV3GJ0AOAZ23A5NuE5hvji-ypXJpiqD822fog/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/1tfNVXVQ3esQw4FySP0kMQiPkBCD_Bd9dwP_rQWbOUSswz4... https://secure-web.cisco.com/1tfNVXVQ3esQw4FySP0kMQiPkBCD_Bd9dwP_rQWbOUSswz4cGOB2TzCmn_v71kFHYK2FEvyKKrZDqwwL_IpLj5LrOyzhzZatukIqXUie48O8Jld4ys_JhH-PYptJ9v1_Uin1jZ4bmMVkbtCjJWYpaooz4qrfWAO_0_S826ay8Cudv7BTfD_1PEPWASGtfSCl5PRhw8IhZV98qdiD7p6saE4cGoDkWYYI311d1UaJasC1KVZYxrrV3GJ0AOAZ23A5NuE5hvji-ypXJpiqD822fog/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
Looks like it downloaded fine. In that case, just move that file to your FS install:
mv fs_install_mcr $FREESURFER_HOME/bin
and you should be good to go.
Best Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Georgia Kapizioni geo.kapizioni@gmail.com Date: Monday, March 1, 2021 at 10:57 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Matlab version 2012b installation problem
External Email - Use Caution Hello Andrew,
Thank you so much for your response.
Here is the output when running the command you suggested:
Georgias-MacBook-Pro:~ georgina$ 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_insta...https://secure-web.cisco.com/1tfNVXVQ3esQw4FySP0kMQiPkBCD_Bd9dwP_rQWbOUSswz4cGOB2TzCmn_v71kFHYK2FEvyKKrZDqwwL_IpLj5LrOyzhzZatukIqXUie48O8Jld4ys_JhH-PYptJ9v1_Uin1jZ4bmMVkbtCjJWYpaooz4qrfWAO_0_S826ay8Cudv7BTfD_1PEPWASGtfSCl5PRhw8IhZV98qdiD7p6saE4cGoDkWYYI311d1UaJasC1KVZYxrrV3GJ0AOAZ23A5NuE5hvji-ypXJpiqD822fog/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.commailto: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.commailto: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_insta...https://secure-web.cisco.com/1tfNVXVQ3esQw4FySP0kMQiPkBCD_Bd9dwP_rQWbOUSswz4cGOB2TzCmn_v71kFHYK2FEvyKKrZDqwwL_IpLj5LrOyzhzZatukIqXUie48O8Jld4ys_JhH-PYptJ9v1_Uin1jZ4bmMVkbtCjJWYpaooz4qrfWAO_0_S826ay8Cudv7BTfD_1PEPWASGtfSCl5PRhw8IhZV98qdiD7p6saE4cGoDkWYYI311d1UaJasC1KVZYxrrV3GJ0AOAZ23A5NuE5hvji-ypXJpiqD822fog/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.commailto: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_insta...https://secure-web.cisco.com/1tfNVXVQ3esQw4FySP0kMQiPkBCD_Bd9dwP_rQWbOUSswz4cGOB2TzCmn_v71kFHYK2FEvyKKrZDqwwL_IpLj5LrOyzhzZatukIqXUie48O8Jld4ys_JhH-PYptJ9v1_Uin1jZ4bmMVkbtCjJWYpaooz4qrfWAO_0_S826ay8Cudv7BTfD_1PEPWASGtfSCl5PRhw8IhZV98qdiD7p6saE4cGoDkWYYI311d1UaJasC1KVZYxrrV3GJ0AOAZ23A5NuE5hvji-ypXJpiqD822fog/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
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 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
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 $FREESURFER_HOME/bin/fs_install_mcr The output is: -rw-r--r-- 1 root wheel 2010 Mar 6 12:03 /Applications/freesurfer/bin/fs_install_mcr
Do you have any idea about what went wrong? Thank you once more time. Best, Georgia
On 1 Mar 2021, at 5:57 PM, Georgia Kapizioni <geo.kapizioni@gmail.commailto:geo.kapizioni@gmail.com> wrote:
Hello Andrew,
Thank you so much for your response.
Here is the output when running the command you suggested:
Georgias-MacBook-Pro:~ georgina$ 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_insta...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.commailto: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.commailto: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_insta...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.commailto: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_insta...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
External Email - Use Caution
Ok I understand.
Thank you for your help. 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 https://secure-web.cisco.com/1Uw8kMcOACw-FvrURLDyTPgouP6SdSvLEnZNwjqUHGSLOq5... https://secure-web.cisco.com/1Uw8kMcOACw-FvrURLDyTPgouP6SdSvLEnZNwjqUHGSLOq5daUPxIiN6uaLQN2M216zLZaao0O12iiaCeL1JpCvzxmrLsCSEy3QpkrRHIzmATgMeFzytHGjquyVagPunwSkUjGZdS2cnlY6OnBl5FUrKiVJGIGqeyr9BbJlXWfQhJnRqqyYVG5Ff0gQoIojew4VYNm_VucvUOD_5vNpiKbbzeqMS6QfbkQdz_fRjerOLPEkcqCN1d-az1eQK4W3vd/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/1Uw8kMcOACw-FvrURLDyTPgouP6SdSvLEnZNwjqUHGSLOq5... https://secure-web.cisco.com/1Uw8kMcOACw-FvrURLDyTPgouP6SdSvLEnZNwjqUHGSLOq5daUPxIiN6uaLQN2M216zLZaao0O12iiaCeL1JpCvzxmrLsCSEy3QpkrRHIzmATgMeFzytHGjquyVagPunwSkUjGZdS2cnlY6OnBl5FUrKiVJGIGqeyr9BbJlXWfQhJnRqqyYVG5Ff0gQoIojew4VYNm_VucvUOD_5vNpiKbbzeqMS6QfbkQdz_fRjerOLPEkcqCN1d-az1eQK4W3vd/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
freesurfer@nmr.mgh.harvard.edu
-
Georgia Kapizioni -
Hoopes, Andrew