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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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