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> > 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> > Rispondi a: Freesurfer support list <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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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