fmriprep: Fatal Bus Error in FMRIPREP

I am runnign fmriprep through singularity. Image was created on 19th March 2019, using tag latest.

When I am running a single subject: I get a fatal Bus Error.

Here is the -vvv debug log when the error occurs.

No resources available
190320-18:01:14,880 nipype.workflow DEBUG:
	 No resources available
190320-18:01:16,878 nipype.workflow DEBUG:
	 No resources available
190320-18:01:18,880 nipype.workflow DEBUG:
	 No resources available
190320-18:01:20,883 nipype.workflow DEBUG:
	 No resources available
190320-18:01:22,407 nipype.workflow INFO:
	 [Node] Finished "_inu_n40".
190320-18:01:22,412 nipype.workflow INFO:
	 [Node] Finished "fmriprep_wf.single_subject_NI9226IM20181130_wf.anat_preproc_wf.brain_extraction_wf.inu_n4".
190320-18:01:22,883 nipype.workflow INFO:
	 [Job 69] Completed (fmriprep_wf.single_subject_NI9226IM20181130_wf.anat_preproc_wf.brain_extraction_wf.inu_n4).
190320-18:01:22,884 nipype.workflow DEBUG:
	 Tasks currently running: 0. Pending: 0.
190320-18:01:22,886 nipype.workflow INFO:
	 [MultiProc] Running 0 tasks, and 6 jobs ready. Free memory (GB): 226.62/226.62, Free processors: 1/1.
190320-18:01:22,978 nipype.workflow DEBUG:
	 Allocating fmriprep_wf.single_subject_NI9226IM20181130_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_preproc ID=70 (0.20GB, 1 threads). Free: 226.42GB, 0 threads.
190320-18:01:22,978 nipype.workflow DEBUG:
	 Setting node inputs
190320-18:01:22,979 nipype.workflow DEBUG:
	 input: source_file
190320-18:01:22,979 nipype.workflow DEBUG:
	 results file: /grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/anat_derivatives_wf/t1_name/result_t1_name.pklz
190320-18:01:22,979 nipype.utils DEBUG:
	 Loading pkl: /grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/anat_derivatives_wf/t1_name/result_t1_name.pklz
190320-18:01:22,980 nipype.workflow DEBUG:
	 output: out
190320-18:01:22,980 nipype.workflow DEBUG:
	 [Node] ds_t1_preproc - setting input source_file = /data/data05/Studies/MCSA/RAW/MRIBIDS/sub-NI9226IM20181130/ses-1/anat/sub-NI9226IM20181130_T1w.nii.gz
190320-18:01:22,980 nipype.workflow DEBUG:
	 input: in_file
190320-18:01:22,980 nipype.workflow DEBUG:
	 results file: /grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/result_inu_n4.pklz
190320-18:01:22,980 nipype.utils DEBUG:
	 Loading pkl: /grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/result_inu_n4.pklz
190320-18:01:22,981 nipype.workflow DEBUG:
	 output: output_image
190320-18:01:22,981 nipype.workflow DEBUG:
	 [Node] ds_t1_preproc - setting input in_file = ['/grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NI9226IM20181130_ses-1_T1w_maths_corrected.nii']
190320-18:01:22,982 nipype.workflow DEBUG:
	 [Node] Directory not found "/grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_preproc".
190320-18:01:22,982 nipype.workflow DEBUG:
	 Checking hash "fmriprep_wf.single_subject_NI9226IM20181130_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_preproc" locally: cached=False, updated=False.
190320-18:01:22,982 nipype.workflow DEBUG:
	 Running node fmriprep_wf.single_subject_NI9226IM20181130_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_preproc on master thread
190320-18:01:22,982 nipype.workflow INFO:
	 [Node] Setting-up "fmriprep_wf.single_subject_NI9226IM20181130_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_preproc" in "/grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_preproc".
190320-18:01:22,982 nipype.workflow DEBUG:
	 [Node] Directory not found "/grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_preproc".
190320-18:01:22,982 nipype.utils DEBUG:
	 Removing contents of /grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_preproc
190320-18:01:22,982 nipype.utils DEBUG:
	 Creating directory /grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_preproc
190320-18:01:23,653 nipype.utils DEBUG:
	 Creating directory /grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_preproc/_report
190320-18:01:24,45 nipype.workflow DEBUG:
	 [Node] Writing pre-exec report to "/grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_preproc/_report/report.rst"
190320-18:01:25,638 nipype.workflow INFO:
	 [Node] Running "ds_t1_preproc" ("smriprep.interfaces.DerivativesDataSink")
190320-18:01:26,386 nipype.utils DEBUG:
	 /data/data05/Studies/MCSA/PROCESSED/FMRI/FMRIPREP/fmriprep/sub-NI9226IM20181130/anat/sub-NI9226IM20181130_desc-preproc_T1w.nii
190320-18:01:26,540 nipype.utils DEBUG:
	 Linking File: /data/data05/Studies/MCSA/PROCESSED/FMRI/FMRIPREP/fmriprep/sub-NI9226IM20181130/anat/sub-NI9226IM20181130_desc-preproc_T1w.nii->/grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NI9226IM20181130_ses-1_T1w_maths_corrected.nii
190320-18:01:26,829 nipype.utils DEBUG:
	 Copying File: /data/data05/Studies/MCSA/PROCESSED/FMRI/FMRIPREP/fmriprep/sub-NI9226IM20181130/anat/sub-NI9226IM20181130_desc-preproc_T1w.nii->/grave/fmriprep_wf/single_subject_NI9226IM20181130_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NI9226IM20181130_ses-1_T1w_maths_corrected.nii
Fatal Python error: Bus error

Thread 0x00007fc04e2d9700 (most recent call first):
  File "/usr/local/miniconda/lib/python3.7/threading.py", line 296 in wait
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/queues.py", line 224 in _feed
  File "/usr/local/miniconda/lib/python3.7/threading.py", line 865 in run
  File "/usr/local/miniconda/lib/python3.7/threading.py", line 917 in _bootstrap_inner
  File "/usr/local/miniconda/lib/python3.7/threading.py", line 885 in _bootstrap

Thread 0x00007fc04eada700 (most recent call first):
  File "/usr/local/miniconda/lib/python3.7/selectors.py", line 415 in select
  File "/usr/local/miniconda/lib/python3.7/multiprocessing/connection.py", line 920 in wait
  File "/usr/local/miniconda/lib/python3.7/concurrent/futures/process.py", line 354 in _queue_management_worker
  File "/usr/local/miniconda/lib/python3.7/threading.py", line 865 in run
  File "/usr/local/miniconda/lib/python3.7/threading.py", line 917 in _bootstrap_inner
  File "/usr/local/miniconda/lib/python3.7/threading.py", line 885 in _bootstrap

Current thread 0x00007fc0766e7700 (most recent call first):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/volumeutils.py", line 833 in _write_data
  File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/volumeutils.py", line 660 in array_to_file
  File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/arraywriters.py", line 562 in to_fileobj
  File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/analyze.py", line 1090 in to_file_map
  File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py", line 334 in to_filename
  File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/bids.py", line 431 in _run_interface
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375 in run
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 637 in _run_command
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 557 in _run_interface
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 473 in run
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 316 in _send_procs_to_workers
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/base.py", line 183 in run
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py", line 599 in run
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 436 in main
  File "/usr/local/miniconda/bin/fmriprep", line 11 in <module>
/var/lib/gridengine/default/spool/alzheimer/job_scripts/109044: line 11:  4051 Bus error

About this issue

  • Original URL
  • State: closed
  • Created 5 years ago
  • Comments: 16 (6 by maintainers)

Most upvoted comments

Also, just in general principle, we should support all valid BIDS datasets with BOLD data, and making people compress their inputs isn’t very user friendly.

+1
effigies on Apr 30, 2019
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