Hi Ileana
Have you examined the input to the mri_normalize call? It should be in the log
file. If it looks normal then maybe tar/gzip the subject dir and send it to us?
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Camerino, I.L. (Ileana)
Sent: Tuesday, May 4, 2021 9:32 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Error 3d normalization pass 1 of 2 white matter peak
External Email - Use Caution
Dear Freesurfer experts,
I am running recon all on a T1 image that already gave me many problems. After
I solved the last one (adding control points in white matter) I finally got a
new error.
The command I run is: echo "cd $PWD; ./recon_all_sub056.sh" | qsub -N
"reconall_sub056" -l walltime=48:00:00,mem=150gb.
Error is: 3d normalization pass 1 of 2 white matter peak found at 110 Cannot
allocate memory Linux dccn-c047.dccn.nl 4.19.94-300.el7.x86_64 #1 SMP Thu Jan 9
16:15:13 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
150gb is more memory than I ever used while running recon all on other data, so
I doubt that adding more memory will help.
Please could someone give me any hint on how can I solve this error?
Thank you in advance
Ileana Camerino
PhD candidate
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognition
Spinozabuilding
Room B02.25
Montessorilaan 3, 6525 HR Nijmegen
The Netherlands
Tel. +31-24 3612618
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Mass General Brigham
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If
the e-mail was sent to you in error but does not contain patient information,
please contact the sender and properly dispose of the e-mail.
Please note that this e-mail is not secure (encrypted). If you do not wish to
continue communication over unencrypted e-mail, please notify the sender of
this message immediately. Continuing to send or respond to e-mail after
receiving this message means you understand and accept this risk and wish to
continue to communicate over unencrypted e-mail.
