External Email - Use Caution        

Hi Andrew
Hope you're well and safe from Covid.
I've got another problem I hope you can help with. When I open a new terminal window I see this, so something's not right, and it's causing other problems.
Did I mess up my path somehow? Or is there something else I need to fix?
(running Mac OS Big Sur 11.0.1 on Macbook Pro 3.3 GHz Dual-Core Intel Core i7)
-------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.1.1
FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Users/jameshartzell/freesurfer
MNI_DIR           /Applications/freesurfer/7.1.1/mni
FSL_DIR           /usr/local/fsl
/etc/zshrc:7: command not found: locale
/etc/zshrc_Apple_Terminal:104: command not found: mkdir
(eval):116: command not found: dirname
(eval):116: command not found: dirname
__add_sys_prefix_to_path:6: command not found: dirname
__add_sys_prefix_to_path:7: command not found: dirname
touch: /Users/jameshartzell/.zsh_sessions/CCE7EE57-B042-4805-8850-D0EBEFD2F650.historynew: No such file or directory

Cheers
James

On Tue, Sep 22, 2020 at 8:40 PM James Hartzell <james.hartzell@gmail.com> wrote:
Okay, great, thanks Andrew.
I can't think of how (otherwise) I might have known not to do that!
Cheers
James

On Tue, Sep 22, 2020 at 8:29 PM Hoopes, Andrew <AHOOPES@mgh.harvard.edu> wrote:

Hi James, please ignore that step. In fact, adding those matlab paths to your default DYLD_LIBRARY_PATH will most likely mess up freesurfer binaries in your environment.

Andrew

 

From: James Hartzell <james.hartzell@gmail.com>
Date: Tuesday, September 22, 2020 at 2:19 PM
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

Thanks, that works just fine.

I'll see if I can figure out how to do the path append part--just something I'm not familiar with doing:

(On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable:

/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.LPxBFTBS/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.LPxBFTBS/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.LPxBFTBS/install-target/v84/bin/maci64:)

Cheers

James

 

On Tue, Sep 22, 2020 at 6:43 PM Hoopes, Andrew <AHOOPES@mgh.harvard.edu> wrote:

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

 

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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

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:

 

 

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

 

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--

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