External Email - Use Caution Dear Freesurfer experts, I continued to go on with my data set using 7.1.0 (with a Catalina MacOS 10.15) and in more than 10% of subjects recon-all -all failed. Failures were always at the segmentation stage (as I showed you in a previous mail) and all these subjects were processed without errors using Freesurfer 6. What do you think is the problem and do you have any suggestion on how to overcome it? Thank you
Angela > Il giorno 28 mag 2020, alle ore 23:18, Angela Favaro <[email protected]> > ha scritto: > > External Email - Use Caution > > > Thank you! > > >> Il giorno 28 mag 2020, alle ore 20:27, Hoopes, Andrew >> <[email protected] <mailto:[email protected]>> 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: <[email protected] >> <mailto:[email protected]>> on behalf of Angela Favaro >> <[email protected] <mailto:[email protected]>> >> Reply-To: FS Help <[email protected] >> <mailto:[email protected]>> >> Date: Wednesday, May 27, 2020 at 4:27 PM >> To: FS Help <[email protected] >> <mailto:[email protected]>> >> 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 <[email protected] <mailto:[email protected]>> >>> Oggetto: [Freesurfer] Longitudinal processing with freesurfer 7.1.0 >>> Data: 23 maggio 2020 10:41:02 CEST >>> A: Freesurfer support list <[email protected] >>> <mailto:[email protected]>> >>> Rispondi a: Freesurfer support list <[email protected] >>> <mailto:[email protected]>> >>> >>> 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 >>> [email protected] <mailto:[email protected]> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] <mailto:[email protected]> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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