External Email - Use Caution Thank you!
> Il giorno 28 mag 2020, alle ore 20:27, Hoopes, Andrew > <ahoo...@mgh.harvard.edu> ha scritto: > > Hi Angela, > > This is a bug on osx, which does not have the --preserve=timestamps flag > available to cp. This will be fixed in the next 7.1 patch, but in the > meantime, you can fix this manually via: > > cd $FREESURFER_HOME/bin > sudo rm rca-long-tp-init > sudo curl > https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init > > <https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-long-tp-init> > -o rca-long-tp-init > sudo chmod +x rca-long-tp-init > > Best > Andrew > > > From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Angela Favaro > <angela.fav...@unipd.it> > Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu> > Date: Wednesday, May 27, 2020 at 4:27 PM > To: FS Help <freesurfer@nmr.mgh.harvard.edu> > Subject: [Freesurfer] Problems with freesurfer 7.1.0 > > External Email - Use Caution > Dear Freesurfer experts, > I am re-analyzing my longitudinal dataset using Freesurfer 7.1.0 with a McOS > Catalina. I found 2 main problems > 1. About a 10% of cases failed at the segmentation stage during the recon-all > processing (I uploaded one of these cases in one of my previous mails) > 2. After the building of the template during the longitudinal processing, at > the recon-all -long I found the following error: > > >> longmc Done >> /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri >> \n cp -f --preserve=timestamps >> /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz >> ./brainmask_template4.mgz \n >> cp: illegal option -- - >> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file >> cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... >> target_directory >> ERROR: >> Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 >> 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64 > > >> recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 >> 03:47:31 CEST 2020 >> >> > > > Can you please help me with this two issues? > Thank you so much! > > Angela > > > > > >> Inizio messaggio inoltrato: >> >> Da: Angela Favaro <angela.fav...@unipd.it <mailto:angela.fav...@unipd.it>> >> Oggetto: [Freesurfer] Longitudinal processing with freesurfer 7.1.0 >> Data: 23 maggio 2020 10:41:02 CEST >> A: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Rispondi a: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> >> External Email - Use Caution >> >> Dear Freesurfer experts, >> I am trying to process a dataset with a longitudinal design. >> However, after building the template, at the “recon-all -long” command I got >> this error: >> >> longmc Done >> /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/mri >> \n cp -f --preserve=timestamps >> /Users/angelafavaro/Desktop/Aachen/template4/mri/brainmask.mgz >> ./brainmask_template4.mgz \n >> cp: illegal option -- - >> usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file target_file >> cp [-R [-H | -L | -P]] [-fi | -n] [-apvXc] source_file ... >> target_directory >> ERROR: >> Darwin iMac-di-Angela.local 19.0.0 Darwin Kernel Version 19.0.0: Thu Oct 17 >> 16:17:15 PDT 2019; root:xnu-6153.41.3~29/RELEASE_X86_64 x86_64 >> >> recon-all -s subj201.long.template4 exited with ERRORS at Sat May 23 >> 03:47:31 CEST 2020 >> >> For more details, see the log file >> /Users/angelafavaro/Desktop/Aachen/subj201.long.template4/scripts/recon-all.log >> >> >> >> >> Thank you for any help! >> >> >> Angela >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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