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]> 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]> > *Date: *Monday, September 21, 2020 at 10:49 AM > *To: *"Hoopes, Andrew" <[email protected]>, FS Help < > [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]> > 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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