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

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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

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