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 chmod +x rca-long-tp-init
Best
Andrew
External Email - Use Caution
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:
/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
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
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?
Inizio messaggio inoltrato:
Oggetto: [Freesurfer] Longitudinal processing with freesurfer 7.1.0
Data: 23 maggio 2020 10:41:02 CEST
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:
/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
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
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