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Anat_airmask pipeline

Compute rotation mask, air mask, artifact mask and hat mask for structural data following step 1 from [Mortamet2009]

  • Adapted from mriqc anatomical workflow.

Pipeline insight

Anat_airmask pipeline combines the following pipelines and processes:
- Rotation mask
- Apply Transform
(default values: interpolation = ‘MultiLabel’)
- Artifact mask
- Get template from templateFlow
(default values : in_template = ‘MNI152NLin2009cAsym’, resolution = 1, suffix = ‘mask’, desc = ‘head’)
Anat airmask pipeline

Mandatory inputs parameters

  • head_mask (a string representing an existing file)

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

    ex. '/home/username/data/raw_data/T1w_brain_outskin.nii'
  • inverse_composite_transform (a string representing an existing file)

    Inverse composite transform used in “ApplyTransform” process (MNI space –> in_file space).

    ex. '/home/username/data/raw_data/T1w_masked_InverseComposite.h5'
  • in_file (a string representing an existing file)

    An anatomical image (T1w or T2w) (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/raw_data/T1w.nii'
  • in_mask (a string representing an existing file)

    Mask image used as reference image in “ApplyTransform” process (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/raw_data/T1w_brain_mask.nii'

Outputs parameters:

  • out_air_mask

    Air mask.

    ex. '/home/username/data/derived_data/air_T1w_mask.nii'
  • out_art_mask

    Artifact mask.

    ex. '/home/username/data/derived_data/art_T1w_mask.nii'
  • out_hat_mask

    Hat mask.

    ex. '/home/username/data/derived_data/hat_T1w_mask.nii'
  • out_rot_mask

    Rotation mask.

    ex. '/home/username/data/derived_data/rot_T1w_mask.nii'

Useful links:

[Mortamet2009]