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ArtifactMask brick

Computes artifact mask

Using the method described in the step 1 (Background Region Segmentation) of the paper of Mortamet and colleagues

Adapted from mriqc anatomical workflow.


Mandatory inputs parameters:

  • in_file (a string representing an existing file)

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

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

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

    ex. '/home/username/data/derived_data/T1w_outskin_mask.nii'
    
  • nasion_post_mask (a string representing an existing file)

    Template mask registered in the in-file space (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/derived_data/t_tpl-MNI152NLin2009cAsym_res-01_desc-head_mask.nii'
    

Optional inputs with default value parameters:

  • suffix (a string, optional, default value is ‘_mask’)

    Suffix of output images.

    ex. '_mask'
    

Optional inputs parameters:

  • rot_mask (a string representing an existing file, optional)

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

    ex. '/home/username/data/derived_data/T1w_rotmasked.nii'
    

Outputs parameters:

  • out_art_mask (a pathlike object or string representing a file)

    Out artifact mask image (extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/derived_data/art_T1w_mask.nii'
    
  • out_hat_mask (a pathlike object or string representing a file)

    Out hat mask image (extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/derived_data/hat_T1w_mask.nii'
    
  • out_air_mask (a pathlike object or string representing a file)

    Out air mask (“hat” mask without artifacts) image (extensions: [.nii, .nii.gz]).

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

Useful links:

Artifactmask mriqc - nipype