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nipreps / mriqc

Automated Quality Control and visual reports for Quality Assessment of structural (T1w, T2w) and functional MRI of the brain
http://mriqc.readthedocs.io
Apache License 2.0
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BIDS filters apparently not working for T1w and T2w #1331

Closed oesteban closed 3 months ago

oesteban commented 3 months ago

What happened?

Running MRIQC with the following filter file:

{
  "bold": {"session": ["pilot20101030", "pilot20001060", "pilot20002030", "pilot20003034"]},
  "dwi": {"session": ["pilot20101030", "pilot20001060", "pilot20002030", "pilot20003034"]},
  "T1w": {"session": ["pilot20101030", "pilot20001060", "pilot20002030", "pilot20003034"]},
  "T2w": {"session": ["pilot20101030", "pilot20001060", "pilot20002030", "pilot20003034"]}
}

resulted in the expected sessions for DWI and BOLD, but all the sessions in the dataset for T1w and T2w.

What command did you use?

mriqc /data/datasets/hcph/ /data/derivatives/hcph/mriqc-24.0.1/ participant --participant-label 001 --nprocs 20 --omp-nthreads 12 -w work3 -vv --bids-database-dir /data/datasets/hcph/.bids-index/ --dsname HCPh --no-sub --bids-filter-file filter.json

What version of the software are you running?

24.0.1

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.

------------------------------------------------------------------
  Running MRIQC version 24.0.1
  ----------------------------------------------------------------
  * BIDS dataset path: /data/datasets/hcph.
  * Output folder: /data/derivatives/hcph/mriqc-24.0.1.
  * Analysis levels: ['participant'].
  * BIDS filters-file: /home/oesteban/tmp/hcph-mriqc/filter.json.
------------------------------------------------------------------

2024-08-20 17:08:57 | IMPORTANT | mriqc            | DataLad dataset identified, attempting to `datalad get` unavailable files.
2024-08-20 17:09:03 | IMPORTANT | mriqc            | Extracting metadata and entities for 84 input runs of modality 't1w'...
2024-08-20 17:09:07 | IMPORTANT | mriqc            | File size ('t1w'): 0.02|0.01 GB [maximum|average].
2024-08-20 17:09:07 | IMPORTANT | mriqc            | Extracting metadata and entities for 85 input runs of modality 't2w'...
2024-08-20 17:09:11 | IMPORTANT | mriqc            | File size ('t2w'): 0.02|0.02 GB [maximum|average].
2024-08-20 17:09:11 | IMPORTANT | mriqc            | Extracting metadata and entities for 2 input runs of modality 'bold'...
2024-08-20 17:09:11 | IMPORTANT | mriqc            | File size ('bold'): 1.74|0.98 GB [maximum|average].
2024-08-20 17:09:11 | IMPORTANT | mriqc            | Extracting metadata and entities for 9 input runs of modality 'dwi'...
2024-08-20 17:09:11 | WARNING  | nipype.workflow  | 5 cannot be processed (too short or too long)
2024-08-20 17:09:11 | IMPORTANT | mriqc            | File size ('dwi'): 0.34|0.10 GB [maximum|average].
2024-08-20 17:09:12 | INFO     | mriqc            | MRIQC config file: /home/oesteban/tmp/hcph-mriqc/work3/config-20240820-170856_dc791d85-6292-4e95-ae5e-cf639f64ca93.toml.
2024-08-20 17:09:16 | IMPORTANT | mriqc            | Building MRIQC's workflows...
2024-08-20 17:09:16 | INFO     | nipype.workflow  | Building functional MRIQC workflow for 2 BOLD runs..
2024-08-20 17:09:17 | INFO     | nipype.workflow  | Building diffusion MRIQC workflow for 4 NIfTI files..
2024-08-20 17:09:17 | INFO     | nipype.workflow  | Building anatomical MRIQC workflow for 169 NIfTI files..
2024-08-20 17:09:23 | IMPORTANT | mriqc            | Workflow building finished (exit code 0)

Additional information / screenshots

No response