Did you run `chmod +x` on the re-downloaded recon-all?
Andrew
From: James Hartzell <[email protected]>
Date: Saturday, September 19, 2020 at 11:09 AM
To: "Hoopes, Andrew" <[email protected]>
Cc: FS Help <[email protected]>
Subject: Re: recon-all 7.1.1
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
<[email protected]<mailto:[email protected]>> 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
<[email protected]<mailto:[email protected]>> wrote:
Hi James,
Try cd`ing to your home directory, then running:
curl
https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon-all
> recon-all
sudo mv recon-all $FREESURFER_HOME/bin
best
Andrew
From: James Hartzell <[email protected]<mailto:[email protected]>>
Date: Saturday, September 19, 2020 at 10:17 AM
To: "Hoopes, Andrew" <[email protected]<mailto:[email protected]>>,
FS Help <[email protected]<mailto:[email protected]>>
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-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
--
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
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