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-all > 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-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