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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.

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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’)

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'
  

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Usefull links:

[Mortamet2009]