ds002169_fmriprep: "ITK ERROR: ITK only supports orthonormal direction cosines."

About half the subjects produced errors like this:

Node: fmriprep_23_2_wf.sub_18_wf.fmap_preproc_wf.wf_auto_00006.brainextraction_wf.n4 Working directory: /node_tmp/work_dir/fmriprep/ds002169_sub-18/fmriprep_23_2_wf/sub_18_wf/fmap_preproc_wf/wf_auto_00006/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/ds002169_sub-18/fmriprep_23_2_wf/sub_18_wf/fmap_preproc_wf/wf_auto_00006/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 (0x56132065fe50)
    Location: "unknown"
    File: /home/conda/feedstock_root/build_artifacts/libitk_1692713128928/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/ds002169_sub-18/fmriprep_23_2_wf/sub_18_wf/fmap_preproc_wf/wf_auto_00006/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/ds002169_sub-18/fmriprep_23_2_wf/sub_18_wf/fmap_preproc_wf/wf_auto_00006/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/ds002169_sub-18/fmriprep_23_2_wf/sub_18_wf/fmap_preproc_wf/wf_auto_00006/brainextraction_wf/n4/clipped_corrected.nii.gz' for output 'output_image' of a N4BiasFieldCorrection interface

poldracklab / tacc-openneuro

ds002169_fmriprep: "ITK ERROR: ITK only supports orthonormal direction cosines." #80