Hi James,

If freesurfer was installed under root, you should prepend sudo to the command to make changes to the directory:

sudo FREESURFER_HOME=$FREESURFER_HOME fs_install_mcr R2014b

best

Andrew

From: James Hartzell <james.hartzell@gmail.com>
Date: Monday, September 21, 2020 at 10:49 AM
To: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edu>, FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: recon-all 7.1.1

        External Email - Use Caution        

Hi Andrew

recon-all appears to have run successfully in 7.1.1, so thanks again for all the guidance.

I've just tried to install the matlab runtime for hipp, amyg, brainstem and thalamic segmentation,

as per

https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime

fs_install_mcr R2014b

the command finished, but indicated a problem with. final renaming requirement:
"On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable:
/var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/runtime/maci64:/var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/sys/os/maci64:/var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/bin/maci64:

(Sep 21, 2020 16:41:29) Exiting with status 0
(Sep 21, 2020 16:41:29) End - Successful.
Finished
mv: rename /var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84 to /Applications/freesurfer/7.1.1/MCRv84: Permission denied
Also, if you could provide guidance for the append step, that would be great.
Cheers
James

On Sat, Sep 19, 2020 at 4:17 PM James Hartzell <james.hartzell@gmail.com> wrote:

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