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Bold_mriqc pipeline

Get no-reference IQMs (image quality metrics) from functional (BOLD) data using mriqc functional workflow (mriqc v22.06)

Disclaimer: A special effort has been made to provide a pipeline in Mia that gives as much as possible the same result as when computing with the native MRIQC. The variation in results between multiple runs of the same inputs is the result of random sampling and floating point precision errors. These variations are usually small, but if an identical result is sought between multiple runs, the environment variable ANTS_RANDOM_SEED should be set (e.g. ANTS_RANDOM_SEED = 1). Further discussion is available in a mia_processes ticket.

Pipeline insight

Bold_mriqc pipeline combines the following pipelines and processes:
- Non steady state detection
- Sanitize
- TSNR
- Mean
- Mask
- Volume registration
(default values : twopass = True, nterpolation = ‘Fourier’)
- MIN align
- IQMs computation
- Plot IQMs
- Func report
Bold_mriqc pipeline

Mandatory inputs parameters

  • func_file (a string representing an existing file)

    A functional image (BOLD). An existing file (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/raw_data/func.nii'

Outputs parameters:

  • func_report

    Functional Image-Quality Metrics summary report.

    ex. '/home/username/data/derived_data/func_ref_functional_mriqcReport_2023_03_31_11_42_10_75.pdf'
  • carpet_seg

    Carpet segmentation.

    ex. '/home/username/data/derived_data/cseg_t_tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz'

Usefull links:

mriqc 22.06