SCORE/SCRUB disabled #278

Jian-uon · 2023-05-09T14:17:12Z

Summary

I used Aslprep in docker to process ASL data, but met an error:

230509-07:12:03,895 nipype.workflow ERROR:
	 could not run node: aslprep_wf.single_subject_101_wf.asl_preproc_run_1_wf.cbf_plot.cbf_ts_summary
230509-07:12:04,85 nipype.workflow CRITICAL:
	 ASLPrep failed: Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.8/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 cbf_ts_summary.

Traceback:
	Traceback (most recent call last):
	  File "/usr/local/miniconda/lib/python3.8/site-packages/numpy/lib/npyio.py", line 985, in _read
	    data = iter(fname)
	TypeError: '_Undefined' object is not iterable

	The above exception was the direct cause of the following exception:

	Traceback (most recent call last):
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 397, in run
	    runtime = self._run_interface(runtime)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/aslprep/interfaces/plotting.py", line 154, in _run_interface
	    fig = CBFtsPlot(
	  File "/usr/local/miniconda/lib/python3.8/site-packages/aslprep/utils/plotting.py", line 128, in __init__
	    volindex = np.loadtxt(scoreindex)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/numpy/lib/npyio.py", line 1356, in loadtxt
	    arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,
	  File "/usr/local/miniconda/lib/python3.8/site-packages/numpy/lib/npyio.py", line 987, in _read
	    raise ValueError(
	ValueError: fname must be a string, filehandle, list of strings,
	or generator. Got <class 'traits.trait_base._Undefined'> instead.


230509-07:12:05,5 cli ERROR:
	 Preprocessing did not finish successfully. Errors occurred while processing data from participants: 101 (2). Check the HTML reports for details.
Sentry is attempting to send 2 pending error messages
Waiting up to 2 seconds

My command

Additional details

ASLPrep version:0.3.0
Docker version: 23.0.5, build bc4487a, MAC OS
Singularity version:

There are two text files in the log folder.

Node: aslprep_wf.single_subject_101_wf.asl_preproc_run_1_wf.parcellate_cbf_wf.warp_atlases_to_asl_space
Working directory: /work/aslprep_wf/single_subject_101_wf/asl_preproc_run_1_wf/parcellate_cbf_wf/warp_atlases_to_asl_space

Node inputs:

args = <undefined>
default_value = 0.0
dimension = 3
environ = {'NSLOTS': '1'}
float = False
input_image = <undefined>
input_image_type = 3
interpolation = GenericLabel
interpolation_parameters = <undefined>
invert_transform_flags = <undefined>
num_threads = 1
out_postfix = _trans
output_image = <undefined>
print_out_composite_warp_file = <undefined>
reference_image = <undefined>
transforms = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 292, in _send_procs_to_workers
    num_subnodes = self.procs[jobid].num_subnodes()
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 1308, in num_subnodes
    self._get_inputs()
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 1322, in _get_inputs
    super(MapNode, self)._get_inputs()
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 619, in _get_inputs
    self.set_input(key, deepcopy(output_value))
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 1157, in set_input
    self._set_mapnode_input(parameter, deepcopy(val))
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 1164, in _set_mapnode_input
    setattr(self._inputs, name, newvalue)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 424, in validate
    value = super(MultiObject, self).validate(objekt, name, newvalue)
  File "/usr/local/miniconda/lib/python3.8/site-packages/traits/trait_types.py", line 2699, in validate
    return TraitListObject(self, object, name, value)
  File "/usr/local/miniconda/lib/python3.8/site-packages/traits/trait_list_object.py", line 582, in __init__
    super().__init__(
  File "/usr/local/miniconda/lib/python3.8/site-packages/traits/trait_list_object.py", line 213, in __init__
    super().__init__(self.item_validator(item) for item in iterable)
  File "/usr/local/miniconda/lib/python3.8/site-packages/traits/trait_list_object.py", line 213, in <genexpr>
    super().__init__(self.item_validator(item) for item in iterable)
  File "/usr/local/miniconda/lib/python3.8/site-packages/traits/trait_list_object.py", line 865, in _item_validator
    return trait_validator(object, self.name, value)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
    value = super(File, self).validate(objekt, name, value, return_pathlike=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
    self.error(objekt, name, str(value))
  File "/usr/local/miniconda/lib/python3.8/site-packages/traits/base_trait_handler.py", line 74, in error
    raise TraitError(
traits.trait_errors.TraitError: Each element of the 'input_image' trait of a DynamicTraitedSpec instance must be a pathlike object or string representing an existing file, but a value of '/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii' <class 'str'> was specified.

Error setting node input:
Node: warp_atlases_to_asl_space
input: input_image
results_file: /work/aslprep_wf/single_subject_101_wf/asl_preproc_run_1_wf/parcellate_cbf_wf/atlas_file_grabber/result_atlas_file_grabber.pklz
value: ['/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/Schaefer2018_100Parcels_17Networks_order_FSLMNI152_2mm.nii', '/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/Schaefer2018_200Parcels_17Networks_order_FSLMNI152_2mm.nii', '/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/Schaefer2018_300Parcels_17Networks_order_FSLMNI152_2mm.nii', '/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/Schaefer2018_400Parcels_17Networks_order_FSLMNI152_2mm.nii', '/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/Schaefer2018_500Parcels_17Networks_order_FSLMNI152_2mm.nii', '/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/Schaefer2018_600Parcels_17Networks_order_FSLMNI152_2mm.nii', '/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/Schaefer2018_700Parcels_17Networks_order_FSLMNI152_2mm.nii', '/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/Schaefer2018_800Parcels_17Networks_order_FSLMNI152_2mm.nii', '/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/Schaefer2018_900Parcels_17Networks_order_FSLMNI152_2mm.nii', '/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/Schaefer2018_1000Parcels_17Networks_order_FSLMNI152_2mm.nii', '/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/glasser360/glasser360MNI.nii.gz', '/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/gordon333/gordon333MNI.nii.gz', '/usr/local/miniconda/lib/python3.8/site-packages/aslprep/data/niftiatlas/TianSubcortical/Tian_Subcortex_S3_3T.nii.gz']


When creating this crashfile, the results file corresponding
to the node could not be found.

Node: aslprep_wf.single_subject_101_wf.asl_preproc_run_1_wf.cbf_plot.cbf_ts_summary
Working directory: /work/aslprep_wf/single_subject_101_wf/asl_preproc_run_1_wf/cbf_plot/cbf_ts_summary

Node inputs:

cbf_ts = <undefined>
conf_file = <undefined>
score_file = <undefined>
seg_file = <undefined>
tr = 2.4

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.8/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 cbf_ts_summary.

Traceback:
	Traceback (most recent call last):
	  File "/usr/local/miniconda/lib/python3.8/site-packages/numpy/lib/npyio.py", line 985, in _read
	    data = iter(fname)
	TypeError: '_Undefined' object is not iterable

	The above exception was the direct cause of the following exception:

	Traceback (most recent call last):
	  File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 397, in run
	    runtime = self._run_interface(runtime)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/aslprep/interfaces/plotting.py", line 154, in _run_interface
	    fig = CBFtsPlot(
	  File "/usr/local/miniconda/lib/python3.8/site-packages/aslprep/utils/plotting.py", line 128, in __init__
	    volindex = np.loadtxt(scoreindex)
	  File "/usr/local/miniconda/lib/python3.8/site-packages/numpy/lib/npyio.py", line 1356, in loadtxt
	    arr = _read(fname, dtype=dtype, comment=comment, delimiter=delimiter,
	  File "/usr/local/miniconda/lib/python3.8/site-packages/numpy/lib/npyio.py", line 987, in _read
	    raise ValueError(
	ValueError: fname must be a string, filehandle, list of strings,
	or generator. Got <class 'traits.trait_base._Undefined'> instead.

About my data:

{"Manufacturer":"Siemens",
"ManufacturersModelName":"Investigational_Device_7T",
"SoftwareVersions":"N4_VE12U_LATEST_20181126",
"MagneticFieldStrength":7,
"ReceiveCoilName":"8Tx32Rx_Head",
"ReceiveCoilActiveElements":"AC",
"PulseSequenceType":"2D_EPI",
"ScanningSequence":"EP",
"SequenceVariant":"SK",
"ScanOptions":"PFP_SAT1_FS",
"SequenceName":"epUHF2d1_98",
"PulseSequenceDetails":"Investigational_Device_7T-syngo_MR_E12",
"MRAcquisitionType":"2D",
"ParallelReductionFactorInPlane":2,
"PartialFourier":0.75,
"PhaseEncodingDirection":"j-",
"EffectiveEchoSpacing":0.000264999783,
"TotalReadoutTime":0.025704978922,
"EchoTime":0.014,
"SliceTiming":[0,0.0325,0.065,0.095,0.1275,0.15999999999,0.19249999999,0.22249999999,0.25499999999,0.28749999999,0.31999999999,0.34999999999,0,0.0325,0.065,0.095,0.1275,0.15999999999,0.19249999999,0.22249999999,0.25499999999,0.28749999999,0.31999999999,0.34999999999],
"DwellTime":0.0000022,
"FlipAngle":90,
"MultibandAccelerationFactor":2,
"RepetitionTimePreparation":2.4,
"ArterialSpinLabelingType":"PASL",
"PostLabelingDelay":1.8,
"BackgroundSuppression":true,
"M0Type":"Separate",
"VascularCrushing":false,
"TotalAcquiredPairs":1,
"BolusCutOffFlag":true,
"PASLType":"FAIR",
"BolusCutOffDelayTime":0.7,
"BolusCutOffTechnique":"QUIPSS"}

The text was updated successfully, but these errors were encountered:

tsalo · 2023-05-09T14:30:56Z

Thanks @Jian-uon. Can you share the command-line call you used as well?

Jian-uon · 2023-05-09T14:34:22Z

Sorry, somehow missed my command.

docker run -v /Users/jianhu/Documents/OSIPI/Dataset6:/data -v /Users/jianhu/Documents/license.txt:/license.txt pennlinc/aslprep /data/rawdata /data/results participant --participant-label 101 -w /work --fs-license-file /license.tx

tsalo · 2023-05-09T14:39:41Z

Thanks!

tsalo · 2023-05-09T20:03:00Z

@Jian-uon I have merged a fix, and it finally just deployed to DockerHub. Would you be willing to try running with the new pennlinc/aslprep:unstable?

Jian-uon · 2023-05-09T20:09:36Z

It's so fast! Sure! Going to run the version you specified. Many thanks for your help!

tsalo · 2023-05-09T20:10:44Z

Please reopen this issue if the same problem crops up, or open a new issue for any new bugs you come across. Thanks for testing out the code.

Jian-uon added the bug Something isn't working label May 9, 2023

tsalo mentioned this issue May 9, 2023

Support runs with SCORE/SCRUB disabled #279

Merged

tsalo closed this as completed in #279 May 9, 2023

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SCORE/SCRUB disabled #278

SCORE/SCRUB disabled #278

Jian-uon commented May 9, 2023 •

edited

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tsalo commented May 9, 2023 •

edited

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Jian-uon commented May 9, 2023

tsalo commented May 9, 2023

tsalo commented May 9, 2023

Jian-uon commented May 9, 2023

tsalo commented May 9, 2023

SCORE/SCRUB disabled #278

SCORE/SCRUB disabled #278

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Jian-uon commented May 9, 2023 • edited Loading

Summary

Additional details

tsalo commented May 9, 2023 • edited Loading

Jian-uon commented May 9, 2023

tsalo commented May 9, 2023

tsalo commented May 9, 2023

Jian-uon commented May 9, 2023

tsalo commented May 9, 2023

Jian-uon commented May 9, 2023 •

edited

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tsalo commented May 9, 2023 •

edited

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