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This is a known issue with this version of FreeSurfer and newer Ubuntu OS.  We hope to have a version of the HCP Pipelines compatible with FreeSurfer 6.0+ in the coming weeks.

Matt.

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Shachar Gal <gal.shachar@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Sunday, January 13, 2019 at 9:46 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] problem using recon-all

        External Email - Use Caution        

hello,
I using the HCP FreeSurfer Pipeline (using FreeSurfer 5.3-HCP version) on ubuntu, and I encounter this error (copying from the recon-all.log)
_______________________________________
#@# Talairach Sun Jan 13 17:35:07 IST 2019
/home/shachar/piano_hcp/102/102/mri

 mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz 

Linux maestro 4.15.0-43-generic #46-Ubuntu SMP Thu Dec 6 14:45:28 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 102 exited with ERRORS at Sun Jan 13 17:35:08 IST 2019 _______________________________________

i'm a bit confused by the lack of error descriptions, and would appreciate any leads for solving it :)

Shachar

 

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