External Email - Use Caution        

Hello James,

Maybe you could do a quick check to see if sudo permission is working for you.

This should always work to create and remove a file….

$ cd /tmp
$ touch foo
$ rm foo

… but sudo has to work for your account to do the same under /Applications

$ cd /tmp
$ sudo touch /Applications/foo
$ sudo rm /Applications/foo

If sudo does not work for you, then you will need to find someone with an account that has sudo privileges.

Assuming sudo works for you in the above example, then you could also try using the bash shell instead of zsh.  Just type “bash" at the terminal to get a bash shell and try the sudo mv command again.  (Zsh is not going to read your .bashrc file if you set it up for Freesurfer, umask, etc.)

$ bash


On Sep 19, 2020, at 10:17, James Hartzell <james.hartzell@gmail.com> wrote:

        External Email - Use Caution        


Hi Andrew

Thanks for the suggestions. I removed freesurfer and reinstalled just 7.1.1.
When I try to run the original patch you suggested I still get permissions problems, even with sudo.

(base) jameshartzell@Jamess-MacBook-Pro ~ % which freesurfer
/Applications/freesurfer/7.1.1/bin/freesurfer

(base) jameshartzell@Jamess-MacBook-Pro freesurfer % cd $FREESURFER_HOME/bin

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo mv recon-all recon-all.backup
Password:

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon-all > recon-all
zsh: permission denied: recon-all

Here's hoping you can send another fix!

Cheers
James



-- 
James Hartzell, PhD (2x) 
Donostia-San Sebatián, Spain
Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy
Center for Buddhist Studies, Columbia University, USA

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