MRIQC pipeline: Fatal Python error

mriqc

#1

I use Python 3.4 to run MRIQC pipleline. However, after I tested two subjects, it gave the same error. The problem seems to be in Nibable module. I would appreciate it if someone can give some hints on how to solve this issue.

Thank you,

Sue

antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /tmp/tmpz7oa0jej/anatMRIQCT1w/SpatialNormalization/_in_file_..s..data3..smri..HCP..pipeline..data..input..WPZOFC_20170524..anat..anat.nii/SpatialNormalization/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 0.01 ] --metric Mattes[ /tmp/tmpz7oa0jej/anatMRIQCT1w/SpatialNormalization/_in_file_..s..data3..smri..HCP..pipeline..data..input..WPZOFC_20170524..anat..anat.nii/SpatialNormalization/fixed_masked.nii.gz, /tmp/tmpz7oa0jej/anatMRIQCT1w/SpatialNormalization/_in_file_..s..data3..smri..HCP..pipeline..data..input..WPZOFC_20170524..anat..anat.nii/SpatialNormalization/moving_masked.nii.gz, 1, 32, Random, 0.15 ] --convergence [ 1000, 1e-06, 20 ] --smoothing-sigmas 4.0vox --shrink-factors 4 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Affine[ 0.08 ] --metric Mattes[ /tmp/tmpz7oa0jej/anatMRIQCT1w/SpatialNormalization/_in_file_..s..data3..smri..HCP..pipeline..data..input..WPZOFC_20170524..anat..anat.nii/SpatialNormalization/fixed_masked.nii.gz, /tmp/tmpz7oa0jej/anatMRIQCT1w/SpatialNormalization/_in_file_..s..data3..smri..HCP..pipeline..data..input..WPZOFC_20170524..anat..anat.nii/SpatialNormalization/moving_masked.nii.gz, 1, 32, Regular, 0.15 ] --convergence [ 500x250x100, 1e-06, 20 ] --smoothing-sigmas 4.0x2.0x0.0vox --shrink-factors 4x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.1, 3.0, 0.0 ] --metric Mattes[ /tmp/tmpz7oa0jej/anatMRIQCT1w/SpatialNormalization/_in_file_..s..data3..smri..HCP..pipeline..data..input..WPZOFC_20170524..anat..anat.nii/SpatialNormalization/fixed_masked.nii.gz, /tmp/tmpz7oa0jej/anatMRIQCT1w/SpatialNormalization/_in_file_..s..data3..smri..HCP..pipeline..data..input..WPZOFC_20170524..anat..anat.nii/SpatialNormalization/moving_masked.nii.gz, 1, 56, Regular, 0.25 ] --convergence [ 50x20, 1e-06, 10 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ]  --write-composite-transform 1
Fatal Python error: Bus error

Current thread 0x00007f5a67561700 (most recent call first):
  File "/usr/lib/python3.4/site-packages/nibabel/volumeutils.py", line 833 in _write_data
  File "/usr/lib/python3.4/site-packages/nibabel/volumeutils.py", line 660 in array_to_file
  File "/usr/lib/python3.4/site-packages/nibabel/arraywriters.py", line 562 in to_fileobj
  File "/usr/lib/python3.4/site-packages/nibabel/analyze.py", line 1069 in to_file_map
  File "/usr/lib/python3.4/site-packages/nibabel/filebasedimages.py", line 338 in to_filename
  File "/usr/lib/python3.4/site-packages/niworkflows/interfaces/utils.py", line 179 in _copyxform
  File "/usr/lib/python3.4/site-packages/niworkflows/interfaces/fixes.py", line 29 in _run_interface
  File "/usr/lib/python3.4/site-packages/niworkflows/nipype/interfaces/base/core.py", line 516 in run
  File "/usr/lib/python3.4/site-packages/niworkflows/interfaces/mni.py", line 220 in _validate_results
  File "/usr/lib/python3.4/site-packages/niworkflows/interfaces/mni.py", line 146 in _run_interface
  File "/usr/lib/python3.4/site-packages/niworkflows/interfaces/report_base.py", line 51 in _run_interface
  File "/usr/lib/python3.4/site-packages/niworkflows/nipype/interfaces/base/core.py", line 516 in run
  File "/usr/lib/python3.4/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 650 in _run_command
  File "/usr/lib/python3.4/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 571 in _run_interface
  File "/usr/lib/python3.4/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 487 in run
  File "/usr/lib/python3.4/site-packages/niworkflows/nipype/pipeline/plugins/linear.py", line 44 in run
  File "/usr/lib/python3.4/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 602 in run
  File "./mriqc_smri.py", line 33 in <module>
Bus error (core dumped)

#2

Hi Sue,

What version of MRIQC are you using? From the error, it looks like you’re running into https://github.com/poldracklab/niworkflows/issues/246, which was fixed in MRIQC 0.12.0.