Dear FreeSurfer community,
I have just installed FreeSurfer v8.0.0 on a 2024 MacBook Pro (M4 Max) and added the license.txt inside the folder.
When I try to open Freeview both on the terminal and by clicking on it, it automatically crashes. Given $FREESURFER_HOME returns zsh: permission denied: /Applications/freesurfer/8.0.0 I’m wondering if perhaps my issue is permission related?
When I go on get info for my folder to check permissions I have the following:
Thanks!
Hi @alba.peris,
Did you check the parent folders to that? E.g., your /Applications and /Applications/freesurfer folder?
Best,
Steven
Do you mean the read & writing permissions?
This is for my /Applications/freesurfer
But for /Applications . Could it be the issue that this is ‘read only’ for everyone? I cannot immediately change the permission for everyone to read & write as my computer is work managed and I don’t have permissions to do so.
Hi @alba.peris,
I can’t exactly say because I do not know how your computer is managed. What about changing the installation directory (and updating FREESURFER_HOME accordingly)?
Best,
Steven
Thanks @Steven !
I have just uninstalled it and trying to install it again in a different folder however it looks like I can only install it for all users on my computer (hence only being able to install it in Applications and not elsewhere).
I’m assuming this is something to do with my permissions on my institution’s laptop and nothing to do with freesurfer?
Thanks,
Alba
Hi @alba.peris,
Does install on a specific disk give you any flexibility? What about just copying the application out of the Application folder?
Best,
Steven
Copying + pasting the freesurfer folder in a directory inside my user worked!!
Thanks very much, @Steven!
Alba
Hi @Steven after the fix from yesterday freeview worked fine!
However today, after successfully running recon-all and segmentHA_T2.sh freeview crashes again and I cannot visualize the outputs.
Actually, after running recon-all I was able to open freeview but after running segmentHA_T2.sh it crashes again. I have tried both on the terminal and by opening the application.
I get the following error:
/Users/ap827/Desktop/Alba/utils/freesurfer/8.0.0/bin/freeview: line 2: 26287 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
/Users/ap827/Desktop/Alba/utils/freesurfer/8.0.0/bin/freeview: line 2: 26287 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
I have tried restarting freesurfer and that did not fix it.
Thanks again,
Alba
Hi @alba.peris,
Where is $FREESURFER_HOME defined? Did you update that environmental variable in your .bash_profile/.bashrc/.zprofile/.zrc (depending on your shell)?
If you did not update the environmental variable after installation, then upon restarting your terminal, your computer will think FreeSurfer is installed in the default FREESURFER_HOME site (which for you is probably in the protected Application folder).
Best,
Steven
Hi @Steven
$FREESURFER_HOME
zsh: permission denied: /Users/ap827/Desktop/Alba/utils/freesurfer/8.0.0
I get this output, but I don’t know why it now should say permission denied? If I look at my rights in the folder I can still read & write.
Can you try to hierachically enter each folder and see which one gets you denied permission?
From ap827 (included) onwards I do seem to have Read & Write permissions.
I’m not sure what has changed as I ran recon_all, checked freeview and in the same terminal ran segmentHA_T2.sh and after that I could no longer open freeview.
I mean in terminal, entering each folder.
Perhaps screenshare will be easier. sent DM.
Following up, we troubleshooted interactively, and it was solved by defining the FreeSurfer environmental variables in the .zprofile.
MANAGED BY INCF