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ds004589-mriqc: "Exception raised while executing Node measures" #90

Open jbwexler opened 2 months ago

jbwexler commented 2 months ago

About half the subjects had similar errors:

Node: mriqc_wf.anatMRIQC.ComputeIQMs.measures
Working directory: /node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/ComputeIQMs/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/measures

Node inputs:

air_msk = /node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/AirMaskWorkflow/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/ArtifactMask/sub-127_T2w_conformed.nii_air.nii.gz
artifact_msk = /node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/AirMaskWorkflow/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/ArtifactMask/sub-127_T2w_conformed.nii_art.nii.gz
head_msk = /node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/HeadMaskWorkflow/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/GradientThreshold/clipped_corrected_enhanced_grad_gradmask.nii.gz
human = True
in_bias = /node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/synthstrip_wf/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/post_n4/clipped_bias.nii.gz
in_file = /node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/conform/sub-127_T2w_conformed.nii.gz
in_fwhm = [1.72787, 5.29946, 1.76725]
in_noinu = /node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/ComputeIQMs/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/harmonize/clipped_corrected_harmonized.nii.gz
in_pvms = ['/node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/brain_tissue_segmentation/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/segmentation/segment_01.nii.gz', '/node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/brain_tissue_segmentation/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/segmentation/segment_02.nii.gz', '/node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/brain_tissue_segmentation/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/segmentation/segment_03.nii.gz']
in_segm = /node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/brain_tissue_segmentation/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/segmentation/segment.nii.gz
in_tpms = <undefined>
mni_tpms = ['/node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/SpatialNormalization/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/tpms_std2t1w/mapflow/_tpms_std2t1w0/tpl-MNI152NLin2009cAsym_res-01_label-CSF_probseg_trans.nii.gz', '/node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/SpatialNormalization/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/tpms_std2t1w/mapflow/_tpms_std2t1w1/tpl-MNI152NLin2009cAsym_res-01_label-GM_probseg_trans.nii.gz', '/node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/SpatialNormalization/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/tpms_std2t1w/mapflow/_tpms_std2t1w2/tpl-MNI152NLin2009cAsym_res-01_label-WM_probseg_trans.nii.gz']
rot_msk = /node_tmp/work_dir/mriqc/ds004589_sub-127/mriqc_wf/anatMRIQC/AirMaskWorkflow/34bee89b5d5e7330fcc7e37ab3fe2ec111724743/RotationMask/sub-127_T2w_conformed_rotmask.nii.gz

Traceback (most recent call last):
  File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 64, in run_node
    result['result'] = node.run(updatehash=updatehash)
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/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 measures.

Traceback:
        Traceback (most recent call last):
          File "/opt/conda/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
            runtime = self._run_interface(runtime)
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
          File "/opt/conda/lib/python3.11/site-packages/mriqc/interfaces/anatomical.py", line 116, in _run_interface
            raise RuntimeError(
        RuntimeError: Input inhomogeneity-corrected data seem empty. MRIQC failed to process this dataset.