See trace below.
Note that --nipype_nb_of_cores
and --openmp_nb_of_cores
parameters not specified, and SR image is well computed and saved.
Inner loop optimization took 96.245 (Unix time)
##########################################################################################################
Writing /output_dir/nipype-1.6.0/sub-ctrl0038/ses-20180912073131/rec-3/srr_pipeline/srtkTVSuperResolution/SRTV_sub-ctrl0038_ses-20180912073131_6V_rad1.nii.gz ... done.
> Write JSON side-car...
> Load SR image /output_dir/nipype-1.6.0/sub-ctrl0038/ses-20180912073131/rec-3/srr_pipeline/srtkTVSuperResolution/SRTV_sub-ctrl0038_ses-20180912073131_6V_rad1.nii.gz...
Image properties: Zooms=(1.125, 1.125, 1.125)/ Shape=(320, 320, 94)/ FOV=[360. 360. 105.75]/ middle cut=[160, 160, 47]
> Crop SR image at (100:220, 100:220, 0:-1)...
Fatal Python error: Segmentation fault
Current thread 0x00007f0a56ad1780 (most recent call first):
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/numpy/linalg/linalg.py", line 1456 in eigh
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nibabel/quaternions.py", line 211 in mat2quat
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nibabel/nifti1.py", line 1031 in set_qform
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nibabel/nifti1.py", line 1817 in _affine2header
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nibabel/spatialimages.py", line 503 in update_header
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nibabel/nifti1.py", line 1807 in update_header
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nibabel/nifti1.py", line 2044 in update_header
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nibabel/spatialimages.py", line 469 in __init__
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nibabel/analyze.py", line 923 in __init__
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nibabel/nifti1.py", line 1772 in __init__
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nibabel/spatialimages.py", line 350 in __getitem__
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/pymialsrtk/interfaces/reconstruction.py", line 422 in _run_interface
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 434 in run
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741 in _run_command
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635 in _run_interface
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516 in run
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 67 in run_node
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/concurrent/futures/process.py", line 239 in _process_worker
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/multiprocessing/process.py", line 99 in run
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/multiprocessing/process.py", line 297 in _bootstrap
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/multiprocessing/popen_fork.py", line 74 in _launch
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/multiprocessing/popen_fork.py", line 20 in __init__
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/multiprocessing/context.py", line 277 in _Popen
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/multiprocessing/process.py", line 112 in start
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/concurrent/futures/process.py", line 607 in _adjust_process_count
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/concurrent/futures/process.py", line 583 in _start_queue_management_thread
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/concurrent/futures/process.py", line 641 in submit
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 175 in _submit_job
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 367 in _send_procs_to_workers
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nipype/pipeline/plugins/base.py", line 184 in run
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py", line 632 in run
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/pymialsrtk/pipelines/anatomical/srr.py", line 679 in run
File "/opt/mialsuperresolutiontoolkit/docker/bidsapp/run.py", line 235 in main
File "/opt/mialsuperresolutiontoolkit/docker/bidsapp/run.py", line 306 in <module>
exception calling callback for <Future at 0x7f09e1868a10 state=finished raised BrokenProcessPool>
Traceback (most recent call last):
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/concurrent/futures/_base.py", line 324, in _invoke_callbacks
callback(self)
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 159, in _async_callback
result = args.result()
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/concurrent/futures/_base.py", line 428, in result
return self.__get_result()
File "/opt/conda/envs/pymialsrtk-env/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.