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 <[email protected]> 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 <[email protected]> > 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 <[email protected]> >> *Date: *Saturday, September 19, 2020 at 10:17 AM >> *To: *"Hoopes, Andrew" <[email protected]>, FS Help < >> [email protected]> >> *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
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