Error in PostFreeSurfer stage

[DavidEWarrenPhD]

I'm getting the following error at the PostFreeSurfer stage after apparently successful PreFreeSurfer and FreeSurfer stages:

terminate called after throwing an instance of 'RBD_COMMON::BaseException'

/opt/HCP-Pipelines/PostFreeSurfer/scripts/FreeSurfer2CaretConvertAndRegisterNonlinear.sh: line 205:  1150 Aborted                 (core dumped) ${MSMBINDIR}/msm --conf=${MSMCONFIGDIR}/MSMSulcStrainFinalconf --inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii --refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii --indata="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii --refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii --out="$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}. --verbose

Traceback (most recent call last):
  File "/run.py", line 349, in <module>
    stage_func()
  File "/run.py", line 114, in run_post_freesurfer
    run(cmd, cwd=args["path"], env={"OMP_NUM_THREADS": str(args["n_cpus"])})
  File "/run.py", line 30, in run
    raise Exception("Non zero return code: %d"%process.returncode)
Exception: Non zero return code: 134

The error occurs with both the latest release version and the dev version. The call is:

docker run -ti --rm -v /mnt/clinical/PrismaQC/2018_12_07/bids:/bids_dir:ro -v ~/Temp/hcpp_output:/output_dir 415ddb225c5b bids_dir output_dir participant --participant_label qc31 --stages PostFreeSurfer --license_key FAKEKEY

Adding --privileged and/or calling with sudo did not change the result. Setting the OMP_NUM_THREADS environment variable explicitly for the docker run call did not change the result.

[DavidEWarrenPhD]

I'm going to close — although this issue is observed when using Docker on lab workstations, we're not seeing it when calling the app through Singularity on the local cluster (where most processing will happen).