Home

Documentation

GitHub

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 registred 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'
  

---

Usefull links:

Artifactmask mriqc - nipype