Il giorno 28 mag 2020, alle ore 20:27, Hoopes, Andrew <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-tp-init -o rca-long-tp-init

sudo chmod +x rca-long-tp-init

 

Best

Andrew

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Angela Favaro <angela.favaro@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.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>

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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer