Input inhomogeneity-corrected data seem empty. MRIQC failed to process this dataset

[galambda]

What happened?

Hi, I received the following error, but not sure what to do about it. The pipeline worked fine for dwi and bold.

Please let me know if you need additional information or the images.

Your help is appreciated.

What command did you use?

mriqc --participant-label KM1001 -m {T1w,T2w} --write-graph --nprocs 20 --mem 40 -v --no-datalad-get --no-sub --notrack bids/ mriqc/ participant

What version of the software are you running?

24.0.2

How are you running this software?

Local installation ("bare-metal")

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

Node: mriqc_wf.anatMRIQC.ComputeIQMs.measures
Working directory: /sc/arion/work/mriqc_wf/anatMRIQC/ComputeIQMs/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/measures

Node inputs:

air_msk = /sc/arion/work/mriqc_wf/anatMRIQC/AirMaskWorkflow/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/ArtifactMask/sub-KM1001_ses-1_inv-01_T1w_conformed.nii_air.nii.gz
artifact_msk = /sc/arion/work/mriqc_wf/anatMRIQC/AirMaskWorkflow/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/ArtifactMask/sub-KM1001_ses-1_inv-01_T1w_conformed.nii_art.nii.gz
head_msk = /sc/arion/work/mriqc_wf/anatMRIQC/HeadMaskWorkflow/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/GradientThreshold/clipped_corrected_enhanced_grad_gradmask.nii.gz
human = True
in_bias = /sc/arion/work/mriqc_wf/anatMRIQC/synthstrip_wf/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/post_n4/clipped_bias.nii.gz
in_file = /sc/arion/work/mriqc_wf/anatMRIQC/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/conform/sub-KM1001_ses-1_inv-01_T1w_conformed.nii.gz
in_fwhm = [2.52802, 2.74467, 2.46006]
in_noinu = /sc/arion/work/mriqc_wf/anatMRIQC/ComputeIQMs/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/harmonize/clipped_corrected_harmonized.nii.gz
in_pvms = ['/sc/arion/work/mriqc_wf/anatMRIQC/brain_tissue_segmentation/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/segmentation/segment_01.nii.gz', '/sc/arion/work/mriqc_wf/anatMRIQC/brain_tissue_segmentation/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/segmentation/segment_02.nii.gz', '/sc/arion/work/mriqc_wf/anatMRIQC/brain_tissue_segmentation/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/segmentation/segment_03.nii.gz']
in_segm = /sc/arion/work/mriqc_wf/anatMRIQC/brain_tissue_segmentation/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/segmentation/segment.nii.gz
in_tpms = <undefined>
mni_tpms = ['/sc/arion/work/mriqc_wf/anatMRIQC/SpatialNormalization/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/tpms_std2t1w/mapflow/_tpms_std2t1w0/tpl-MNI152NLin2009cAsym_res-01_label-CSF_probseg_trans.nii.gz', '/sc/arion/work/mriqc_wf/anatMRIQC/SpatialNormalization/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/tpms_std2t1w/mapflow/_tpms_std2t1w1/tpl-MNI152NLin2009cAsym_res-01_label-GM_probseg_trans.nii.gz', '/sc/arion/work/mriqc_wf/anatMRIQC/SpatialNormalization/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/tpms_std2t1w/mapflow/_tpms_std2t1w2/tpl-MNI152NLin2009cAsym_res-01_label-WM_probseg_trans.nii.gz']
rot_msk = /sc/arion/work/mriqc_wf/anatMRIQC/AirMaskWorkflow/2a5aea4ac5304e55d777f0b9ad7dadcfe069d77c/RotationMask/sub-KM1001_ses-1_inv-01_T1w_conformed_rotmask.nii.gz

Traceback (most recent call last):
  File "/sc/arion/work/envs/mriqc/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 64, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/sc/arion/work/envs/mriqc/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
    result = self._run_interface(execute=True)
  File "/sc/arion/work/envs/mriqc/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
    return self._run_command(execute)
  File "/sc/arion/work/neukap01/dcm2bids-env/envs/mriqc/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node measures.

Traceback:
	Traceback (most recent call last):
	  File "/sc/arion/work/envs/mriqc/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 401, in run
	    runtime = self._run_interface(runtime)
	  File "/sc/arion/work/envs/mriqc/lib/python3.9/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.

Additional information / screenshots

No response

[effigies]

Can you add a screenshot of your anatomical image(s)?

[galambda]

Of course, here you are.

[hfxcarl]

@galambda Your file naming doesn't seem to match the actual image contrast. For example, your sub-KM1001_ses-1_T1w.nii.gz looks like a T2w image. Correct filenaming will allow MRIQC to use the contrast-specific template images and their associated masks for processing, ie., T2w to tpl-MNI152NLin2009cAsym_res-01_T2w.nii.gz

[galambda]

Hi @hfxcarl, I renamed the image you suggested and after this didn't work, I also tried renaming the inv-01_T1w to inv-01_T2w, but that also didn't help as you can see below.

What else can I try?

Node: mriqc_wf.anatMRIQC.ComputeIQMs.measures
Working directory: /sc/arion/work/mriqc_wf/anatMRIQC/ComputeIQMs/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/measures

Node inputs:

air_msk = /sc/arion/work/mriqc_wf/anatMRIQC/AirMaskWorkflow/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/ArtifactMask/sub-KM1001_ses-2_inv-01_T2w_conformed.nii_air.nii.gz
artifact_msk = /sc/arion/work/mriqc_wf/anatMRIQC/AirMaskWorkflow/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/ArtifactMask/sub-KM1001_ses-2_inv-01_T2w_conformed.nii_art.nii.gz
head_msk = /sc/arion/work/mriqc_wf/anatMRIQC/HeadMaskWorkflow/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/GradientThreshold/clipped_corrected_enhanced_grad_gradmask.nii.gz
human = True
in_bias = /sc/arion/work/mriqc_wf/anatMRIQC/synthstrip_wf/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/post_n4/clipped_bias.nii.gz
in_file = /sc/arion/work/mriqc_wf/anatMRIQC/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/conform/sub-KM1001_ses-2_inv-01_T2w_conformed.nii.gz
in_fwhm = [2.50735, 2.7835, 2.52172]
in_noinu = /sc/arion/work/mriqc_wf/anatMRIQC/ComputeIQMs/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/harmonize/clipped_corrected_harmonized.nii.gz
in_pvms = ['/sc/arion/work/mriqc_wf/anatMRIQC/brain_tissue_segmentation/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/segmentation/segment_01.nii.gz', '/sc/arion/work/mriqc_wf/anatMRIQC/brain_tissue_segmentation/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/segmentation/segment_02.nii.gz', '/sc/arion/work/mriqc_wf/anatMRIQC/brain_tissue_segmentation/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/segmentation/segment_03.nii.gz']
in_segm = /sc/arion/work/mriqc_wf/anatMRIQC/brain_tissue_segmentation/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/segmentation/segment.nii.gz
in_tpms = <undefined>
mni_tpms = ['/sc/arion/work/mriqc_wf/anatMRIQC/SpatialNormalization/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/tpms_std2t1w/mapflow/_tpms_std2t1w0/tpl-MNI152NLin2009cAsym_res-01_label-CSF_probseg_trans.nii.gz', '/sc/arion/work/mriqc_wf/anatMRIQC/SpatialNormalization/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/tpms_std2t1w/mapflow/_tpms_std2t1w1/tpl-MNI152NLin2009cAsym_res-01_label-GM_probseg_trans.nii.gz', '/sc/arion/work/mriqc_wf/anatMRIQC/SpatialNormalization/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/tpms_std2t1w/mapflow/_tpms_std2t1w2/tpl-MNI152NLin2009cAsym_res-01_label-WM_probseg_trans.nii.gz']
rot_msk = /sc/arion/work/mriqc_wf/anatMRIQC/AirMaskWorkflow/83a6fb3ea3c61bf5c5160104522b16b4bc9b008a/RotationMask/sub-KM1001_ses-2_inv-01_T2w_conformed_rotmask.nii.gz

Traceback (most recent call last):
  File "/sc/arion/work/envs/mriqc/lib/python3.9/site-packages/mriqc/engine/plugin.py", line 64, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/sc/arion/work/envs/mriqc/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
    result = self._run_interface(execute=True)
  File "/sc/arion/work/envs/mriqc/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
    return self._run_command(execute)
  File "/sc/arion/work/envs/mriqc/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node measures.

Traceback:
	Traceback (most recent call last):
	  File "/sc/arion/work/envs/mriqc/lib/python3.9/site-packages/nipype/interfaces/base/core.py", line 401, in run
	    runtime = self._run_interface(runtime)
	  File "/sc/arion/work/envs/mriqc/lib/python3.9/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.

[jbwexler]

I've been seeing this error in a number of datasets as well. Happy to share more if that would be helpful.

[weberam2]

I think I'm having the same issue
I believe my issue is related to T2starw files I have:

sub-REGPTC115_ses-1_part-mag_T2starw.json
sub-REGPTC115_ses-1_part-mag_T2starw.nii.gz
sub-REGPTC115_ses-1_part-phase_T2starw.json
sub-REGPTC115_ses-1_part-phase_T2starw.nii.gz
sub-REGPTC115_ses-1_T1w.json
sub-REGPTC115_ses-1_T1w.nii.gz
sub-REGPTC115_ses-1_T2w.json
sub-REGPTC115_ses-1_T2w.nii.gz

When I run with the -m T1w flag, MRIQC runs successfully

What command did you use?

docker run -it --rm -v $PWD:/data:ro -v $PWD/derivatives/mriqc:/out nipreps/mriqc:latest /data /out participant --participant_label REGPTC115

What version of the software are you running?

Running MRIQC version 25.1.0.dev45+g699d1691

How are you running this software?

docker

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

------------------------------------------------------------------
  Running MRIQC version 25.1.0.dev45+g699d1691
  ----------------------------------------------------------------

  NOTICE
  Copyright © The NiPreps Developers.

  This product includes software developed by
  the NiPreps Community (https://nipreps.org/).

  Portions of this software were developed at the Department of
  Psychology at Stanford University, Stanford, CA, US.

  This software contains code ultimately derived from the
  PCP Quality Assessment Protocol (QAP;
  http://preprocessed-connectomes-project.org/quality-assessment-protocol)
  by C. Craddock, S. Giavasis, D. Clark, Z. Shezhad, and J. Pellman.

  This software is also distributed as a Docker container image.
  The bootstrapping file for the image ("Dockerfile") is licensed
  under the MIT License.

  ----------------------------------------------------------------

  * BIDS dataset path: /data.
  * Output folder: /out.
  * Analysis levels: ['participant'].
------------------------------------------------------------------

2025-07-14 19:56:07 | IMPORTANT | mriqc            | Extracting metadata and entities for 2 input runs of modality 't1w'...
2025-07-14 19:56:07 | IMPORTANT | mriqc            | File size ('t1w'): 0.03|0.03 GB [maximum|average].
2025-07-14 19:56:07 | IMPORTANT | mriqc            | Extracting metadata and entities for 6 input runs of modality 't2w'...
2025-07-14 19:56:07 | IMPORTANT | mriqc            | File size ('t2w'): 0.00|0.00 GB [maximum|average].
2025-07-14 19:56:12 | IMPORTANT | mriqc            | Building MRIQC's workflows...
2025-07-14 19:56:16 | IMPORTANT | mriqc            | Workflow building finished (exit code 0).
2025-07-14 19:56:19 | WARNING  | mriqc            | IMPORTANT: Anonymized quality metrics (IQMs) will be submitted to MRIQC's metrics repository. Submission of IQMs can be disabled using the ``--no-sub`` argument. Please visit https://mriqc.readthedocs.io/en/latest/dsa.html to revise MRIQC's Data Sharing Agreement.
2025-07-14 19:59:12 | INFO     | niworkflows      | Estimating initial transform using AffineInitializer
2025-07-14 19:59:14 | INFO     | niworkflows      | Estimating initial transform using AffineInitializer
2025-07-14 19:59:14 | INFO     | niworkflows      | Estimating initial transform using AffineInitializer
2025-07-14 19:59:18 | INFO     | niworkflows      | Estimating initial transform using AffineInitializer
2025-07-14 19:59:20 | INFO     | niworkflows      | Estimating initial transform using AffineInitializer
2025-07-14 19:59:22 | INFO     | niworkflows      | Estimating initial transform using AffineInitializer
2025-07-14 19:59:50 | INFO     | niworkflows      | Loading settings from file /opt/conda/lib/python3.11/site-packages/niworkflows/data/t1w-mni_registration_testing_000.json.
2025-07-14 19:59:50 | INFO     | niworkflows      | Retry #1, commandline:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/dcb61cdc3e37ab9e3bec0dec422e708f20729301/SpatialNormalization/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 1.0 ] --metric Mattes[ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/dcb61cdc3e37ab9e3bec0dec422e708f20729301/SpatialNormalization/fixed_masked.nii.gz, /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/dcb61cdc3e37ab9e3bec0dec422e708f20729301/SpatialNormalization/moving_masked.nii.gz, 1, 56, Random, 0.2 ] --convergence [ 20, 1e-07, 15 ] --smoothing-sigmas 4.0vox --shrink-factors 2 --use-histogram-matching 0 --transform Affine[ 1.0 ] --metric Mattes[ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/dcb61cdc3e37ab9e3bec0dec422e708f20729301/SpatialNormalization/fixed_masked.nii.gz, /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/dcb61cdc3e37ab9e3bec0dec422e708f20729301/SpatialNormalization/moving_masked.nii.gz, 1, 56, Random, 0.1 ] --convergence [ 15, 1e-08, 5 ] --smoothing-sigmas 2.0vox --shrink-factors 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.995 ]  --write-composite-transform 1
2025-07-14 19:59:53 | INFO     | niworkflows      | Loading settings from file /opt/conda/lib/python3.11/site-packages/niworkflows/data/t1w-mni_registration_testing_000.json.
2025-07-14 19:59:53 | INFO     | niworkflows      | Retry #1, commandline:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/97260cdfda32140caed8d560644a76d3581389da/SpatialNormalization/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 1.0 ] --metric Mattes[ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/97260cdfda32140caed8d560644a76d3581389da/SpatialNormalization/fixed_masked.nii.gz, /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/97260cdfda32140caed8d560644a76d3581389da/SpatialNormalization/moving_masked.nii.gz, 1, 56, Random, 0.2 ] --convergence [ 20, 1e-07, 15 ] --smoothing-sigmas 4.0vox --shrink-factors 2 --use-histogram-matching 0 --transform Affine[ 1.0 ] --metric Mattes[ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/97260cdfda32140caed8d560644a76d3581389da/SpatialNormalization/fixed_masked.nii.gz, /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/97260cdfda32140caed8d560644a76d3581389da/SpatialNormalization/moving_masked.nii.gz, 1, 56, Random, 0.1 ] --convergence [ 15, 1e-08, 5 ] --smoothing-sigmas 2.0vox --shrink-factors 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.995 ]  --write-composite-transform 1
2025-07-14 19:59:53 | INFO     | niworkflows      | Terminal outputs of initialization saved (/tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/81a86948096162e69474439fc79d60d827b76949/SpatialNormalization/stderr.nipype-init).
2025-07-14 19:59:53 | INFO     | niworkflows      | Loading settings from file /opt/conda/lib/python3.11/site-packages/niworkflows/data/t1w-mni_registration_testing_000.json.
2025-07-14 19:59:53 | INFO     | niworkflows      | Retry #1, commandline:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/81a86948096162e69474439fc79d60d827b76949/SpatialNormalization/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 1.0 ] --metric Mattes[ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/81a86948096162e69474439fc79d60d827b76949/SpatialNormalization/fixed_masked.nii.gz, /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/81a86948096162e69474439fc79d60d827b76949/SpatialNormalization/moving_masked.nii.gz, 1, 56, Random, 0.2 ] --convergence [ 20, 1e-07, 15 ] --smoothing-sigmas 4.0vox --shrink-factors 2 --use-histogram-matching 0 --transform Affine[ 1.0 ] --metric Mattes[ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/81a86948096162e69474439fc79d60d827b76949/SpatialNormalization/fixed_masked.nii.gz, /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/81a86948096162e69474439fc79d60d827b76949/SpatialNormalization/moving_masked.nii.gz, 1, 56, Random, 0.1 ] --convergence [ 15, 1e-08, 5 ] --smoothing-sigmas 2.0vox --shrink-factors 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.995 ]  --write-composite-transform 1
2025-07-14 19:59:58 | INFO     | niworkflows      | Loading settings from file /opt/conda/lib/python3.11/site-packages/niworkflows/data/t1w-mni_registration_testing_000.json.
2025-07-14 19:59:58 | INFO     | niworkflows      | Retry #1, commandline:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/da31e41d1fbaa8f801ce7dff3c1698162b44c19a/SpatialNormalization/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 1.0 ] --metric Mattes[ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/da31e41d1fbaa8f801ce7dff3c1698162b44c19a/SpatialNormalization/fixed_masked.nii.gz, /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/da31e41d1fbaa8f801ce7dff3c1698162b44c19a/SpatialNormalization/moving_masked.nii.gz, 1, 56, Random, 0.2 ] --convergence [ 20, 1e-07, 15 ] --smoothing-sigmas 4.0vox --shrink-factors 2 --use-histogram-matching 0 --transform Affine[ 1.0 ] --metric Mattes[ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/da31e41d1fbaa8f801ce7dff3c1698162b44c19a/SpatialNormalization/fixed_masked.nii.gz, /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/da31e41d1fbaa8f801ce7dff3c1698162b44c19a/SpatialNormalization/moving_masked.nii.gz, 1, 56, Random, 0.1 ] --convergence [ 15, 1e-08, 5 ] --smoothing-sigmas 2.0vox --shrink-factors 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.995 ]  --write-composite-transform 1
2025-07-14 19:59:58 | INFO     | niworkflows      | Loading settings from file /opt/conda/lib/python3.11/site-packages/niworkflows/data/t1w-mni_registration_testing_000.json.
2025-07-14 19:59:58 | INFO     | niworkflows      | Retry #1, commandline:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/767eaec83be4e23a6cf016b9e621b33bbe0fb6ad/SpatialNormalization/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 1.0 ] --metric Mattes[ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/767eaec83be4e23a6cf016b9e621b33bbe0fb6ad/SpatialNormalization/fixed_masked.nii.gz, /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/767eaec83be4e23a6cf016b9e621b33bbe0fb6ad/SpatialNormalization/moving_masked.nii.gz, 1, 56, Random, 0.2 ] --convergence [ 20, 1e-07, 15 ] --smoothing-sigmas 4.0vox --shrink-factors 2 --use-histogram-matching 0 --transform Affine[ 1.0 ] --metric Mattes[ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/767eaec83be4e23a6cf016b9e621b33bbe0fb6ad/SpatialNormalization/fixed_masked.nii.gz, /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/767eaec83be4e23a6cf016b9e621b33bbe0fb6ad/SpatialNormalization/moving_masked.nii.gz, 1, 56, Random, 0.1 ] --convergence [ 15, 1e-08, 5 ] --smoothing-sigmas 2.0vox --shrink-factors 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.995 ]  --write-composite-transform 1
2025-07-14 20:00:02 | INFO     | niworkflows      | Successful spatial normalization (retry #1).
2025-07-14 20:00:02 | INFO     | niworkflows      | Loading settings from file /opt/conda/lib/python3.11/site-packages/niworkflows/data/t1w-mni_registration_testing_000.json.
2025-07-14 20:00:02 | INFO     | niworkflows      | Retry #1, commandline:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 0 --initial-moving-transform [ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/2c8b35ff41b975cf9c9b64ab6cc1c88112bbcf88/SpatialNormalization/transform.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ ants_t1_to_mni, ants_t1_to_mni_Warped.nii.gz ] --transform Rigid[ 1.0 ] --metric Mattes[ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/2c8b35ff41b975cf9c9b64ab6cc1c88112bbcf88/SpatialNormalization/fixed_masked.nii.gz, /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/2c8b35ff41b975cf9c9b64ab6cc1c88112bbcf88/SpatialNormalization/moving_masked.nii.gz, 1, 56, Random, 0.2 ] --convergence [ 20, 1e-07, 15 ] --smoothing-sigmas 4.0vox --shrink-factors 2 --use-histogram-matching 0 --transform Affine[ 1.0 ] --metric Mattes[ /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/2c8b35ff41b975cf9c9b64ab6cc1c88112bbcf88/SpatialNormalization/fixed_masked.nii.gz, /tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/2c8b35ff41b975cf9c9b64ab6cc1c88112bbcf88/SpatialNormalization/moving_masked.nii.gz, 1, 56, Random, 0.1 ] --convergence [ 15, 1e-08, 5 ] --smoothing-sigmas 2.0vox --shrink-factors 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.995 ]  --write-composite-transform 1
2025-07-14 20:00:03 | INFO     | niworkflows      | Report - setting fixed (/tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/dcb61cdc3e37ab9e3bec0dec422e708f20729301/SpatialNormalization/fixed_masked.nii.gz) and moving (/tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/dcb61cdc3e37ab9e3bec0dec422e708f20729301/SpatialNormalization/ants_t1_to_mni_Warped.nii.gz) images
2025-07-14 20:00:03 | INFO     | niworkflows      | Generating visual report
2025-07-14 20:00:04 | INFO     | niworkflows      | Successful spatial normalization (retry #1).
2025-07-14 20:00:05 | INFO     | niworkflows      | Successful spatial normalization (retry #1).
2025-07-14 20:00:05 | INFO     | niworkflows      | Report - setting fixed (/tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/97260cdfda32140caed8d560644a76d3581389da/SpatialNormalization/fixed_masked.nii.gz) and moving (/tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/97260cdfda32140caed8d560644a76d3581389da/SpatialNormalization/ants_t1_to_mni_Warped.nii.gz) images
2025-07-14 20:00:05 | INFO     | niworkflows      | Generating visual report
2025-07-14 20:00:06 | INFO     | niworkflows      | Report - setting fixed (/tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/81a86948096162e69474439fc79d60d827b76949/SpatialNormalization/fixed_masked.nii.gz) and moving (/tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/81a86948096162e69474439fc79d60d827b76949/SpatialNormalization/ants_t1_to_mni_Warped.nii.gz) images
2025-07-14 20:00:06 | INFO     | niworkflows      | Generating visual report
2025-07-14 20:00:09 | INFO     | niworkflows      | Successful spatial normalization (retry #1).
2025-07-14 20:00:10 | INFO     | niworkflows      | Successful spatial normalization (retry #1).
2025-07-14 20:00:10 | INFO     | niworkflows      | Report - setting fixed (/tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/da31e41d1fbaa8f801ce7dff3c1698162b44c19a/SpatialNormalization/fixed_masked.nii.gz) and moving (/tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/da31e41d1fbaa8f801ce7dff3c1698162b44c19a/SpatialNormalization/ants_t1_to_mni_Warped.nii.gz) images
2025-07-14 20:00:10 | INFO     | niworkflows      | Generating visual report
2025-07-14 20:00:11 | INFO     | niworkflows      | Report - setting fixed (/tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/767eaec83be4e23a6cf016b9e621b33bbe0fb6ad/SpatialNormalization/fixed_masked.nii.gz) and moving (/tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/767eaec83be4e23a6cf016b9e621b33bbe0fb6ad/SpatialNormalization/ants_t1_to_mni_Warped.nii.gz) images
2025-07-14 20:00:11 | INFO     | niworkflows      | Generating visual report
2025-07-14 20:00:14 | INFO     | niworkflows      | Successful spatial normalization (retry #1).
2025-07-14 20:00:15 | INFO     | niworkflows      | Report - setting fixed (/tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/2c8b35ff41b975cf9c9b64ab6cc1c88112bbcf88/SpatialNormalization/fixed_masked.nii.gz) and moving (/tmp/work/mriqc_wf/anatMRIQC/SpatialNormalization/2c8b35ff41b975cf9c9b64ab6cc1c88112bbcf88/SpatialNormalization/ants_t1_to_mni_Warped.nii.gz) images
2025-07-14 20:00:15 | INFO     | niworkflows      | Generating visual report
/opt/conda/lib/python3.11/site-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
  return _methods._mean(a, axis=axis, dtype=dtype,
/opt/conda/lib/python3.11/site-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
  ret = ret.dtype.type(ret / rcount)
2025-07-14 20:00:58 | WARNING  | nipype.workflow  | Storing result file without outputs
2025-07-14 20:00:58 | WARNING  | nipype.workflow  | [Node] Error on "mriqc_wf.anatMRIQC.ComputeIQMs.measures" (/tmp/work/mriqc_wf/anatMRIQC/ComputeIQMs/dcb61cdc3e37ab9e3bec0dec422e708f20729301/measures)
2025-07-14 20:00:58 | ERROR    | nipype.workflow  | Node measures.a2 (taskid=114) crashed: /out/logs/crash-20250714-200058-root-measures.a2-4e66455e-cef2-4c62-9b98-752bb2a590a5.txt
Traceback (most recent call last):
  File "/opt/conda/bin/mriqc", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/mriqc/cli/run.py", line 188, in main
    mriqc_wf.run(**_plugin)
  File "/opt/conda/lib/python3.11/site-packages/nipype/pipeline/engine/workflows.py", line 638, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 196, in run
    notrun.append(self._clean_queue(jobid, graph, result=result))
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.11/site-packages/mriqc/engine/plugin.py", line 259, in _clean_queue
    raise RuntimeError(''.join(result['traceback']))
RuntimeError: 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.

[galambda]

Hi @jbwexler any help is appreciated, as this affected also @weberam2.

[jbwexler]

As a starting point, here are the OpenNeuro datasets that produced this error on one or more subjects:

ds005603
ds003814
ds004712
ds005576
ds003691
ds005464
ds005003
ds004627
ds005237
ds004856
ds004466
ds003836
ds005386

[jbwexler]

It looks like all of these besides ds003691 contain T2w images, so maybe the issue is related to that? ds003691 contains two kinds of T1w images: "acq-orig" and "acq-hcHighres", in case that's useful.