ds002738-fmriprep: "Description: ITK ERROR: ITK only supports orthonormal direction cosines. No orthonormal definition found!"

[jbwexler]

About half the subjects had similar errors. Rerunning didn't fix.

Node: fmriprep_23_2_wf.sub_119_wf.bold_task_rest_wf.bold_fit_wf.unwarp_wf.brainextraction_wf.n4
Working directory: /node_tmp/work_dir/fmriprep/ds002738_sub-119/fmriprep_23_2_wf/sub_119_wf/bold_task_rest_wf/bold_fit_wf/unwarp_wf/brainextraction_wf/n4

Node inputs:

args =
bias_image =
bspline_fitting_distance =
bspline_order =
convergence_threshold = 1e-07
copy_header = True
dimension = 3
environ = {'NSLOTS': '8'}
histogram_sharpening =
input_image =
mask_image =
n_iterations = [50, 50, 50, 50, 50]
num_threads = 8
output_image =
rescale_intensities = False
save_bias = False
shrink_factor = 4
weight_image =

Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node n4.

Cmdline:
N4BiasFieldCorrection -d 3 --input-image /node_tmp/work_dir/fmriprep/ds002738_sub-119/fmriprep_23_2_wf/sub_119_wf/bold_task_rest_wf/bold_fit_wf/unwarp_wf/brainextraction_wf/clipper_pre/clipped.nii.gz --convergence [ 50x50x50x50x50, 1e-07 ] --output clipped_corrected.nii.gz --shrink-factor 4
Stdout:

Stderr:
Exception caught during reference file reading

    itk::ExceptionObject (0x55f0e2353170)
    Location: "unknown"

sub-278: 01:00:23 failed: 0
sub-309: 00:58:22 failed: 0
sub-290: 01:01:43 failed: 0
Node: fmriprep_23_2_wf.sub_119_wf.bold_task_rest_wf.bold_fit_wf.unwarp_wf.brainextraction_wf.n4
Working directory: /node_tmp/work_dir/fmriprep/ds002738_sub-119/fmriprep_23_2_wf/sub_119_wf/bold_task_rest_wf/bold_fit_wf/unwarp_wf/brainextraction_wf/n4

Node inputs:

args =
bias_image =
bspline_fitting_distance =
bspline_order =
convergence_threshold = 1e-07
copy_header = True
dimension = 3
environ = {'NSLOTS': '8'}
histogram_sharpening =
input_image =
mask_image =
n_iterations = [50, 50, 50, 50, 50]
num_threads = 8
output_image =
rescale_intensities = False
save_bias = False
shrink_factor = 4
weight_image =

Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node n4.

Cmdline:
N4BiasFieldCorrection -d 3 --input-image /node_tmp/work_dir/fmriprep/ds002738_sub-119/fmriprep_23_2_wf/sub_119_wf/bold_task_rest_wf/bold_fit_wf/unwarp_wf/brainextraction_wf/clipper_pre/clipped.nii.gz --convergence [ 50x50x50x50x50, 1e-07 ] --output clipped_corrected.nii.gz --shrink-factor 4
Stdout:

Stderr:
Exception caught during reference file reading

    itk::ExceptionObject (0x55f0e2353170)
    Location: "unknown"
    File: /home/conda/feedstock_root/build_artifacts/libitk_1701488084194/work/Modules/IO/NIFTI/src/itkNiftiImageIO.cxx
    Line: 2016
    Description: ITK ERROR: ITK only supports orthonormal direction cosines.  No orthonormal definition found!

     file /node_tmp/work_dir/fmriprep/ds002738_sub-119/fmriprep_23_2_wf/sub_119_wf/bold_task_rest_wf/bold_fit_wf/unwarp_wf/brainextraction_wf/clipper_pre/clipped.nii.gz
    Segmentation fault

Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs
setattr(outputs, key, val)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'output_image' trait of a N4BiasFieldCorrectionOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/node_tmp/work_dir/fmriprep/ds002738_sub-119/fmriprep_23_2_wf/sub_119_wf/bold_task_rest_wf/bold_fit_wf/unwarp_wf/brainextraction_wf/n4/clipped_corrected.nii.gz' <class 'str'> was specified.

    During handling of the above exception, another exception occurred:

    Traceback (most recent call last):
      File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 398, in run
        runtime = self._post_run_hook(runtime)
      File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/mixins/fixheader.py", line 127, in _post_run_hook
        outputs = self.aggregate_outputs(runtime=runtime).get_traitsfree()
      File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 460, in aggregate_outputs
        raise FileNotFoundError(msg)
    FileNotFoundError: No such file or directory '/node_tmp/work_dir/fmriprep/ds002738_sub-119/fmriprep_23_2_wf/sub_119_wf/bold_task_rest_wf/bold_fit_wf/unwarp_wf/brainextraction_wf/n4/clipped_corrected.nii.gz' for output 'output_image' of a N4BiasFieldCorrection interface