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CarpetParcellation brick

Dilate brainmask, subtract from itself then generate the union of obtained crown mask and epi parcellation

Adapted from mriqc, niworkflow binary dilatation, niworkflow binary Subtraction.


Mandatory inputs parameters:

  • brain_mask (a string representing an existing file)

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

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

    Template carpet register in subject space (valid extensions: [.nii, .nii.gz]).

    ex. '/home/username/data/raw_data/t_tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz'
    

Optional inputs with default value parameters:

  • out_prefix (a string, optional, default value is ‘cseg’)

    Specify the string to be prepended to the segmentation filename of the output file.

    ex. 'cseg_'
    

Outputs parameters:

  • out_file (a strings representing a file)

    Carpet parcelattion file (extensions: [.nii, .nii.gz])

    ex. '/home/username/data/derived_data/cseg_t_tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz'
    

Useful links:

niworkflow binary dilatation, niworkflow binary subtraction