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BoldQMs brick

Computes the functional Image Quality Metrics (IQMs) as defined in mriqc v22.06

A no-reference IQM is a measurement of some aspect of the actual image which cannot be compared to a reference value for the metric since there is no ground-truth about what this number should be. All the computed IQMs corresponding to an image are saved in a JSON file.

Adapted from mriqc.

Mandatory inputs parameters:

  • in_epi (a string representing an existing file)

    Mean bold image (valid extensions: [.nii, .nii.gz]).

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

Optional inputs with default value parameters:

  • in_fd_thresh (a float, optional, default value is 0.2)

    Motion threshold for FD computation

    ex. 0.2

Optional inputs:

  • in_dummy_TRs (an integer , optional)

    Number of dummy scans.

    ex. 2
  • in_dvars_file (a string representing an existing file, optional)

    DVARS file.

    ex. '/home/username/data/derived_data/dvars_reg_func_valid.out'
  • in_fd_file (a string representing an existing file, optional)

    FD file.

    ex. '/home/username/data/derived_data/fd_reg_func_valid_oned.out'
  • in_fwhm_file (a string representing an existing file, optional)

    A file with FWHM information.

    ex. '/home/username/data/derived_data/fwhm_mean_reg_func_valid.out'
  • in_gcor (a float)

    Global correlation value.

    ex. 0.0612
  • in_hmc” (a string representing an existing file, optional)

    Motion corrected input image (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/derived_data/reg_func_valid.nii'
  • in_mask (a string representing an existing file, optional)

    Brain mask (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/derived_data/automask_reg_func_valid.nii'
  • in_outliers_file (a string representing an existing file, optional)

    Outliers file.

    ex. '/home/username/data/derived_data/outliers_reg_func_valid.out'
  • in_QI_file (a string representing an existing file, optional)

    Quality index file.

    ex. '/home/username/data/derived_data/QI_reg_func_valid.out'
  • in_spikes_file (a string representing an existing file, optional)

    Spikes file.

    ex. '/home/username/data/derived_data/spikes_reg_func_valid.out'
  • in_tsnr (a string representing an existing file, optional)

    tSNR input volume. (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/derived_data/reg_func_valid_tsnr.nii'

Outputs parameters:

  • out_file (a strings representing a file)

    A json file with all the IQMs computed.

    ex. '/home/username/data/derived_data/mean_reg_func_valid_functional_qc.json'

Useful links:

mriqc func qc