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Seems like you're running out of memory when using more than 1 threads. Can you allocate more memory to the VM? You can also try running Synthseg without the --robust flag? ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Giulio Siracusano giuliosiracusano@gmail.com Sent: Monday, May 1, 2023 4:16 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] SynthSeg terminates with 'std::bad_alloc' error when using --threads option (>1)
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Hello experts, I've installed FreeSurfer 7.3.2 and used SynthSeg with --parc --robust and --threads options. The Virtual Machine I use has 4 cores and 20GB of ram, running Ubuntu 18.04. I've executed the same command without --threads option and it works perfectly, even running 4 different subjects at the time. As usual, I've used as input NIFTI archives of raw scans (one .nii file per subject) But, If I run one single subject with SynthSeg and I use --threads option >1, it terminates with the error underneath:
SynthSeg-robust 2.0 using 4 threads predicting 1/1 terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped)
I've tested with 4, 3, 2 threads and it doesn't work. I've also checked for memory allocation and the maximum it reaches is approx 50%, before terminating. I use tensorflow-cpu==2.12.0
Any help is appreciated
Regards
GS