hello Freesurfer developers,
during the recon-all (autorecon1) processing, it seems that the mne_nu_correct procedure does not always manage to finish successfully. I have searched the net, found a question in the mailing list, which seemed to be similar, but no answer (http://www.bic.mni.mcgill.ca/pipermail/minc-users/2015-November/004205.html).
Our status file shows, that we had sometimes runs which were completed without errors. Maybe, we should not have started the recon-all a second time. It would be very great if you could help with further hints. For instance, could we remove a file or several files to roll back to the situation when it worked?
all the best, Burkhard
.....................
FREESURFER_VERSION: freesurfer-x86_64-unknown-linux-gnu-stable5-20130513 Platform: ubuntu 16.04 (xfce)
uname -a
Linux ren 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Command: freesurfer=5.3.0_maess@ren:/scr/eber2/intstats > recon-all -autorecon1 -nuintensitycor-3T -subjid is09
-- Dr. Burkhard Maess Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511 mail: maess 'at' cbs.mpg.de, http://www.cbs.mpg.de
Ubuntu 16 comes with a version of perl that is compatible with the MNI tools shipped with the version of freesurfer you are using.
The easiest way to remedy the situation is to download and install the development version of freesurfer which fixes this issue and will be included in the upcoming 6.0 release (see "Development Version"):
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
-Zeke
On 10/17/2016 09:28 AM, Burkhard Maess wrote:
hello Freesurfer developers,
during the recon-all (autorecon1) processing, it seems that the mne_nu_correct procedure does not always manage to finish successfully. I have searched the net, found a question in the mailing list, which seemed to be similar, but no answer (http://www.bic.mni.mcgill.ca/pipermail/minc-users/2015-November/004205.html).
Our status file shows, that we had sometimes runs which were completed without errors. Maybe, we should not have started the recon-all a second time. It would be very great if you could help with further hints. For instance, could we remove a file or several files to roll back to the situation when it worked?
all the best, Burkhard
.....................
FREESURFER_VERSION: freesurfer-x86_64-unknown-linux-gnu-stable5-20130513 Platform: ubuntu 16.04 (xfce)
uname -a
Linux ren 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Command: freesurfer=5.3.0_maess@ren:/scr/eber2/intstats > recon-all -autorecon1 -nuintensitycor-3T -subjid is09
-- Dr. Burkhard Maess Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511 mail: maess 'at' cbs.mpg.de, http://www.cbs.mpg.de
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Oops, I meant to write "Ubuntu 16 comes with a version of perl that is *incompatible* with the MNI tools..."
On 10/18/2016 10:03 AM, Z K wrote:
Ubuntu 16 comes with a version of perl that is compatible with the MNI tools shipped with the version of freesurfer you are using.
The easiest way to remedy the situation is to download and install the development version of freesurfer which fixes this issue and will be included in the upcoming 6.0 release (see "Development Version"):
https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
-Zeke
On 10/17/2016 09:28 AM, Burkhard Maess wrote:
hello Freesurfer developers,
during the recon-all (autorecon1) processing, it seems that the mne_nu_correct procedure does not always manage to finish successfully. I have searched the net, found a question in the mailing list, which seemed to be similar, but no answer (http://www.bic.mni.mcgill.ca/pipermail/minc-users/2015-November/004205.html).
Our status file shows, that we had sometimes runs which were completed without errors. Maybe, we should not have started the recon-all a second time. It would be very great if you could help with further hints. For instance, could we remove a file or several files to roll back to the situation when it worked?
all the best, Burkhard
.....................
FREESURFER_VERSION: freesurfer-x86_64-unknown-linux-gnu-stable5-20130513 Platform: ubuntu 16.04 (xfce)
uname -a
Linux ren 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
Command: freesurfer=5.3.0_maess@ren:/scr/eber2/intstats > recon-all -autorecon1 -nuintensitycor-3T -subjid is09
-- Dr. Burkhard Maess Max Planck Institute for Human Cognitive and Brain Sciences Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511 mail: maess 'at' cbs.mpg.de, http://www.cbs.mpg.de
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
freesurfer@nmr.mgh.harvard.edu
-
Burkhard Maess -
Z K