External Email - Use Caution
Hi Andrew
There's still some sort of problem:
(base) jameshartzell@Jamess-MacBook-Pro freesurfer % which freesurfer /Applications/freesurfer/7.1.1/bin/freesurfer
(base) jameshartzell@Jamess-MacBook-Pro freesurfer % recon-all -s $S -i $S....nii.gz -autorecon1 zsh: permission denied: recon-all zsh: permission denied: recon-all zsh: command not found: zsh:
Cheers James
On Sat, Sep 19, 2020 at 5:03 PM James Hartzell james.hartzell@gmail.com wrote:
Hi Andrew
Thanks, cool, that looks like it worked. I'll run recon-all, check the logs and QA tools and let you know if I come across any issues.
Cheers James
On Sat, Sep 19, 2020 at 4:36 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:
Hi James,
Try cd`ing to your home directory, then running:
curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon...
recon-all
sudo mv recon-all $FREESURFER_HOME/bin
best
Andrew
*From: *James Hartzell james.hartzell@gmail.com *Date: *Saturday, September 19, 2020 at 10:17 AM *To: *"Hoopes, Andrew" AHOOPES@mgh.harvard.edu, FS Help < freesurfer@nmr.mgh.harvard.edu> *Subject: *recon-all 7.1.1
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...
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
-- 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