External Email - Use Caution
Dear freesurfer experts, I found the same problems with recon-all (segmentation failure) using a Mac OS Sierra (10.12) and the same failures (more than 10% of cases) with the command: recon-all -base template -tp subj001 -tp subj002 -all
Hope it is possible to find a solution Thank you
Angela
Il giorno 30 mag 2020, alle ore 12:47, Angela Favaro angela.favaro@unipd.it ha scritto:
External Email - Use CautionDear 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 <angela.favaro@unipd.it mailto:angela.favaro@unipd.it> ha scritto:
External Email - Use CautionThank you!
Il giorno 28 mag 2020, alle ore 20:27, Hoopes, Andrew <AHOOPES@mgh.harvard.edu mailto:AHOOPES@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... 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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Angela Favaro <angela.favaro@unipd.it mailto:angela.favaro@unipd.it> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Date: Wednesday, May 27, 2020 at 4:27 PM To: FS Help <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Problems with freesurfer 7.1.0
External Email - Use CautionDear Freesurfer experts, I am re-analyzing my longitudinal dataset using Freesurfer 7.1.0 with a McOS Catalina. I found 2 main problems
- 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)
- 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.favaro@unipd.it mailto:angela.favaro@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 CautionDear 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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