External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Giulio Siracusano
<giuliosiracus...@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)
External Email - Use Caution
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
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