Harmonize brick¶
Harmonize input image using a white matter mask¶
As described in the method to compute the arfifact mask described in the paper of Mortamet and colleagues Be carrefull, if the suffix and prefix input parameters are not defined or consist only of one or more white spaces, the input parameter will be overwritten.
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'
- wm_mask (a string representing an existing file)
White matter mask file (valid extensions: [.nii, .nii.gz]).
ex. 'home/username/data/derived_data/T1w_seg.nii'
Optional inputs with default value parameters:
- erodemask (a boolean, optional, default value is True)
Erode mask.
ex. True
- prefix (a string, optional, default value is ‘’)
Prefix of the output image.
ex. ''
- suffix (a string, optional, default value is ‘_harmonized’)
Suffix of output image.
ex. '_harmonized'
Outputs parameters:
- out_file (a strings representing a file)
Path of the harmonized image (extensions: [.nii, .nii.gz]).
ex. '/home/username/data/derived_data/T1w_harmonized.nii'
Useful links: