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
The Talairach transform step will fail at the mri_nu_correct.mni command on newer Linux distributions that come with perl version 5.22 (and higher) due to an incompatibility with the mni tools shipped with FreeSurfer v5.3 and newer versions of perl. The issue has been fixed in the Development Version of FreeSurfer which is normally available from the following link:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev
However, we are currently experiencing a system wide hardware failure on our network file servers and hope to have the issues resolved in a day or so. Thanks for you patience.
-Zeke
On 06/28/2016 07:14 AM, Mikael Novén wrote:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Mikael Novén -
Z K