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 <[email protected]> Date: Tuesday, September 22, 2020 at 2:19 PM To: "Hoopes, Andrew" <[email protected]> Cc: FS Help <[email protected]> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> Date: Monday, September 21, 2020 at 10:49 AM To: "Hoopes, Andrew" <[email protected]<mailto:[email protected]>>, FS Help <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- 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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