macapype.pipelines.extract_brain.create_extract_pipe

macapype.pipelines.extract_brain.create_extract_pipe(params_template, params={}, name='extract_pipe')

Description: Extract T1 brain using AtlasBrex

Params:

• norm_intensity (see N4BiasFieldCorrection for arguments)

• atlas_brex (see AtlasBREX for arguments) - also available as indiv_params

Inputs:

inputnode:

restore_T1:

preprocessed (debiased/denoised) T1 file name

restore_T2:

preprocessed (debiased/denoised)T2 file name

arguments:

params_template:

dictionary of info about template

params:

dictionary of node sub-parameters (from a json file)

name:

pipeline name (default = “extract_pipe”)

Outputs:

smooth_mask.out_file:

Computed mask (after some smoothing)