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AnatIQMs brick

Computes the anatomical 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_ras (a string representing an existing file)

    Input anatomical image (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/raw_data/T1w.nii'

Optional inputs with default value parameters:

  • airmask (a string representing an existing file)

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

    ex. '/home/username/data/derived_data/air_T1w_mask.nii'
  • artmask (a string representing an existing file)

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

    ex. '/home/username/data/derived_data/art_T1w_mask.nii'
  • hatmask (a string representing an existing file)

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

    ex. '/home/username/data/derived_data/hat_T1w_mask.nii'
  • headmask (a string representing an existing file)

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

    ex. '/home/username/data/derived_data/n4c_T1w_clipped_brain_outskin_mask.nii'
  • in_fwhm (a string representing an existing file)

    A file with FWHM information.

    ex. '/home/username/data/derived_data/fwhm_T1w.out'
  • in_inu (a string representing an existing file)

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

    ex. '/home/username/data/derived_data/n4c_T1w_clipped_bias.nii'
  • in_noinu (a string representing an existing file)

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

    ex. '/home/username/data/derived_data/n4c_T1w_clipped_harmonized.nii'
  • mni_tpms (a list with items which are string representing an existing file)

    Templates registered in the subject space (valid extensions: [.nii, .nii.gz]).

    ex. ['/home/username/data/derived_data/csf_tpl-MNI152NLin2009cAsym_res-01_label-CSF_probseg.nii.gz', '/home/username/data/derived_data/gm_tpl-MNI152NLin2009cAsym_res-01_label-GM_probseg.nii.gz', '/home/username/data/derived_data/wm_tpl-MNI152NLin2009cAsym_res-01_label-WM_probseg.nii.gz']
  • pvms (a list with items which are string representing an existing file)

    Tissues probality map (valid extensions: [.nii, .nii.gz]).

    ex. ['/home/username/data/derived_data/ss_n4c_T1w_clippep_pve_0.nii', '/home/username/data/derived_data/ss_n4c_T1w_clippep_pve_1.nii', '/home/username/data/derived_data/ss_n4c_T1w_clippep_pve_2.nii'
  • rotmask (a string representing an existing file)

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

    ex. '/home/username/data/derived_data/T1w_rotmasked.nii'
  • segmentation (a string representing an existing file)

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

    ex. '/home/username/data/derived_data/ss_n4c_T1w_clippep_seg.nii'

Outputs parameters:

  • out_file (a strings representing a file)

    A json file with all the IQMs computed.

    ex. '/home/username/data/derived_data/T1w_anat_qc.json'

Useful links:

mriqc Anat qc