Summary of what happened:
Hello! I have been able to run ASLPrep on a longitudinal dataset that I am collecting, but each run exits with the same error: “nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node extract_deltam.”
I do not believe that all the proper outputs are being created due to this error. My ASL files contain the m0 image and 7 label/control pairs, but unfortunately we also have a dummy control scan in between m0 and the first label/control pair and I wonder if this is throwing the deltam calculation.
Thanks for your help!
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run -B /zwork/hannah/mbp/data:/bids-root
-B /zwork/hannah/mbp/data/derivatives/aslprep:/output
-B /zwork/hannah/mbp/workdir:/workdir
-B /sw/freesurfer/license.txt:/license
/zwork/hannah/mbp/data/code/aslprep/aslprep-0.7.2.simg
/bids-root
/output
participant
--participant_label sub-1001B
-w /workdir
--fs-license-file /license
--longitudinal
Version:
0.7.2
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity container on a shared computing cluster
Data formatted according to a validatable standard? Please provide the output of the validator:
1: [WARN] It is recommended to define 'VascularCrushing' for this file. 'VascularCrushing' is a boolean value indicating if an ASL crusher method is used. (code: 137 - VASCULAR_CRUSHING_MUST_DEFINE)
./sub-1001B/ses-base1/perf/sub-1001B_ses-base1_asl.nii.gz
./sub-1001B/ses-base2/perf/sub-1001B_ses-base2_asl.nii.gz
./sub-1001B/ses-gest1/perf/sub-1001B_ses-gest1_asl.nii.gz
./sub-1001B/ses-gest2/perf/sub-1001B_ses-gest2_asl.nii.gz
./sub-1001B/ses-gest3/perf/sub-1001B_ses-gest3_asl.nii.gz
./sub-1001B/ses-gest4/perf/sub-1001B_ses-gest4_asl.nii.gz
./sub-1001B/ses-gest5/perf/sub-1001B_ses-gest5_asl.nii.gz
./sub-1001B/ses-gest6/perf/sub-1001B_ses-gest6_asl.nii.gz
./sub-1001B/ses-gest7/perf/sub-1001B_ses-gest7_asl.nii.gz
./sub-1001B/ses-post1/perf/sub-1001B_ses-post1_asl.nii.gz
... and 1 more files having this issue (Use --verbose to see them all).
Please visit https://neurostars.org/search?q=VASCULAR_CRUSHING_MUST_DEFINE for existing conversations about this issue.
2: [WARN] The recommended file /README is very small. Please consider expanding it with additional information about the dataset. (code: 213 - README_FILE_SMALL)
./README
Please visit https://neurostars.org/search?q=README_FILE_SMALL for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
1557 Files, 88.46GB rest MRI
12 - Subjects TODO: full task name for rest
23 - Sessions
Relevant log outputs (up to 20 lines):
File: /output/sub-1001B/log/20240715-142821_2f6583ad-d957-4227-ba1a-657a20410788/crash-20240716-003951-hannah-extract_deltam-682c3d1b-dee7-4e01-8430-cae8f81f7d48.txt
Working Directory: /workdir/aslprep_0_7_wf/sub_1001B_wf/asl_preproc_ses_post2_wf/cbf_wf/extract_deltam
Inputs:
asl_file: /workdir/aslprep_0_7_wf/sub_1001B_wf/asl_preproc_ses_post2_wf/asl_native_wf/aslref_asl/sub-1001B_ses-post2_asl_reducedresampled.nii.gz
aslcontext: /workdir/aslprep_0_7_wf/sub_1001B_wf/asl_preproc_ses_post2_wf/asl_native_wf/reduce_asl_file/sub-1001B_ses-post2_aslcontext_reduced.tsv
dummy_scans: 0
fwhm: 5.0
in_mask: /workdir/aslprep_0_7_wf/sub_1001B_wf/asl_preproc_ses_post2_wf/cbf_wf/reduce_mask/sub-1001B_ses-post2_asl_contrast_squeezed_corrected_brain_mask_maths_refinemask.nii.gz
m0scan:
m0scan_metadata: None
metadata: {'AcquisitionMatrixPE': 63, 'AcquisitionNumber': 1, 'AcquisitionTime': '14:16:40.485000', 'AcquisitionVoxelSize': [2.5, 2.5, 2.5], 'ArterialSpinLabelingType': 'PCASL', 'BackgroundSuppression': False, 'BaseResolution': 96, 'BodyPartExamined': 'BRAIN', 'CoilCombinationMethod': 'Sum of Squares', 'ConsistencyInfo': 'N4_VE11C_LATEST_20160120', 'ConversionSoftware': 'dcm2niix', 'ConversionSoftwareVersion': 'v1.0.20220720', 'DeviceSerialNumber': '67022', 'DwellTime': 2e-06, 'EchoTime': 0.03676, 'EchoTrainLength': 63, 'FlipAngle': 120, 'HeudiconvVersion': '1.1.6', 'ImageOrientationPatientDICOM': [0.998922, -0.0389219, -0.0253158, 0.0343595, 0.986394, -0.160766], 'ImageOrientationText': 'Tra>Cor(-9.2)>Sag(-1.8)', 'ImageType': ['ORIGINAL', 'PRIMARY', 'ASL', 'NONE', 'ND', 'MOSAIC'], 'ImagingFrequency': 123.198, 'InPlanePhaseEncodingDirectionDICOM': 'COL', 'InstitutionAddress': 'UCEN Rd 551 Bldg 251,Isla Vista,Los Angeles,US,93117', 'InstitutionName': 'UCSB Brain Imaging Center', 'InstitutionalDepartmentName': 'Psych Department', 'LabelingDuration': 1.5, 'M0Type': 'Included', 'MRAcquisitionType': '3D', 'MagneticFieldStrength': 3, 'Manufacturer': 'Siemens', 'ManufacturersModelName': 'Prisma_fit', 'MatrixCoilMode': 'SENSE', 'MeanGzx10': 6, 'Modality': 'MR', 'NonlinearGradientCorrection': False, 'PartialFourier': 1, 'PatientPosition': 'HFS', 'PercentPhaseFOV': 100, 'PercentSampling': 65.625, 'PhaseEncodingDirection': 'j-', 'PhaseEncodingSteps': 63, 'PhaseResolution': 0.65625, 'PixelBandwidth': 2605, 'PostLabelingDelay': 1.8, 'ProcedureStepDescription': 'Jacobs^Grotzinger', 'ProtocolName': 'tgse_pcasl_PLD1800_ucsd', 'PulseSequenceDetails': '%CustomerSeq%\\tgse_pcasl_ve11c_Multidelay', 'RFGap': 0.00036, 'ReceiveCoilActiveElements': 'HC1-7', 'ReceiveCoilName': 'HeadNeck_64', 'ReconMatrixPE': 96, 'RepetitionTime': 4.1, 'RepetitionTimePreparation': 4100, 'SAR': 0.0559364, 'ScanOptions': 'FS', 'ScanningSequence': 'EP', 'SequenceName': 'tgse3d1_3780', 'SequenceVariant': 'SK', 'SeriesDescription': 'tgse_pcasl_PLD1800_ucsd', 'SeriesNumber': 10, 'ShimSetting': [-4122, 1379, -5954, 367, 148, -292, -167, 51], 'SliceThickness': 2.5, 'SoftwareVersions': 'syngo MR E11', 'SpacingBetweenSlices': 2.5, 'StationName': 'MRC35273', 'TotalAcquiredPairs': 7, 'TxRefAmp': 212.175}
name_source: /bids-root/sub-1001B/ses-post2/perf/sub-1001B_ses-post2_asl.nii.gz
Traceback (most recent call last):
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/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 extract_deltam.
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/interfaces/cbf.py", line 240, in _run_interface
assert len(label_volume_idx) == len(control_volume_idx)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AssertionError
Screenshots / relevant information:
Here are the contents of the aslcontext.tsv files for each session (the first control image is the dummy scan):
volume_type
m0scan
control
label
control
label
control
label
control
label
control
label
control
label
control
label
control