Did you run `chmod +x` on the re-downloaded recon-all?

Andrew

From: James Hartzell <james.hartzell@gmail.com>
Date: Saturday, September 19, 2020 at 11:09 AM
To: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>
Cc: FS Help <freesurfer@nmr.mgh.harvard.edu>
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 <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-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

--

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