Dear Freesurfer Developers,
I'm attempting to process high resolution images on a new system and following https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon I at first try to run downsampled (1x1x1 mm) images. recon-all suddenly stops during #@# Talairach with no error codes except for the "exited with ERRORS" message. I'm a bit clueless as to what could be wrong. The images are from a Philips 7T Achieva system and have been normalized using ANTS N4BiasFieldCorrectionImageFilter() before attempting recon-all (though uncorrected gives the same resulting error). I thought that there was a problem with the permissions so I changed the default using setfacl which seems to work but no change.
OUTPUT: INFO: extension is mgz #-------------------------------------------- #@# Talairach tis 28 jun 2016 12:52:35 CEST /usr/local/freesurfer/subjects/106_1/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux mikael-Aspire-VN7-591G 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 106_1 exited with ERRORS at tis 28 jun 2016 12:52:36 CEST"
BUILD-STAMP: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
OPERATING SYSTEM: No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 16.04 LTS Release: 16.04 Codename: xenial
UNAME -A OUTPUT: Linux mikael-Aspire-VN7-591G 4.4.0-24-generic #43-Ubuntu SMP Wed Jun 8 19:27:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Log file included.
Thank you very much for your help.
All the best, Mikael Novén