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 -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
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