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: