Hi, I have been trying to run mriqc (v0.15.2rc1) for a small dataset of about 60 subjects on a slurm cluster (for each node I give 16G memory).
I get an error while processing T1 images for one subject. Anyone knows why this is happening?
The system log:
[Node] Finished “workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize”.
2020-02-22 09:41:04,434 nipype.workflow:INFO [Node] Finished “workflow_enumerator.anatMRIQCT1w.ComputeIQMs.harmonize”.
2020-02-22 09:41:09,822 py.warnings:WARNING /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range.
warnings.warn(“No contour levels were found”
200222-09:41:14,429 nipype.workflow INFO:
[Node] Finished “workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotSegmentation”.
2020-02-22 09:41:14,429 nipype.workflow:INFO [Node] Finished “workflow_enumerator.anatMRIQCT1w.ReportsWorkflow.PlotSegmentation”.
200222-09:41:16,658 nipype.workflow ERROR:
could not run node: workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization.a0
2020-02-22 09:41:16,658 nipype.workflow:ERROR could not run node: workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization.a0
Traceback (most recent call last):
File “/usr/local/miniconda/bin/mriqc”, line 10, in
sys.exit(main())
File “/usr/local/miniconda/lib/python3.7/site-packages/mriqc/bin/mriqc_run.py”, line 256, in main
mriqc_wf.run(**plugin_settings)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py”, line 599, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/base.py”, line 191, in run
report_nodes_not_run(notrun)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/tools.py”, line 82, in report_nodes_not_run
raise RuntimeError(('Workflow did not execute cleanly. ’
RuntimeError: Workflow did not execute cleanly. Check log for details
The internal log:
ode: workflow_enumerator.anatMRIQCT1w.SpatialNormalization.SpatialNormalization
Working directory: /mriqc_work/workflow_enumerator/anatMRIQCT1w/SpatialNormalization/in_file…data…sub-FMR024…anat…sub-FMR024_run-1_T1w.nii.gz/SpatialNormalization
Node inputs:
compress_report = auto
explicit_masking = True
flavor = fast
float = False
initial_moving_transform =
lesion_mask =
moving = T1w
moving_image = /mriqc_work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/in_file…data…sub-FMR024…anat…sub-FMR024_run-1_T1w.nii.gz/inu_n4/sub-FMR024_run-1_T1w_conformed_corrected.nii.gz
moving_mask = /mriqc_work/workflow_enumerator/anatMRIQCT1w/AFNISkullStripWorkflow/in_file…data…sub-FMR024…anat…sub-FMR024_run-1_T1w.nii.gz/binarize/sub-FMR024_run-1_T1w_conformed_calc_thresh.nii.gz
num_threads = 1
orientation = RAS
out_report = report.svg
reference = T1w
reference_image =
reference_mask = /home/vincentq/singularity_tmp/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz
settings =
template = MNI152NLin2009cAsym
template_resolution = 2
template_spec =
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 69, in run_node
result[‘result’] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 472, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 563, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 643, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 375, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/mni.py”, line 187, in _run_interface
‘Robust spatial normalization failed after %d retries.’ % (self.retry - 1))
RuntimeError: Robust spatial normalization failed after 1 retries.
stderr.nipype-init
bad det -1 v 1 u -1
bad det -1 v 1 u -1 new 1
output.nipype
Bus error (core dumped)