macapype.pipelines.segment.create_segment_atropos_pipe

macapype.pipelines.segment.create_segment_atropos_pipe(params={}, name='segment_atropos_pipe')

Description: Segmentation with ANTS atropos script

Params:

• Atropos (see AtroposN4)

• threshold_gm, threshold_wm, threshold_csf (see Threshold for arguments)

Inputs:

inputnode:

brain_file: T1 image, after extraction and norm bin_norm_intensity

gm_prior_file: grey matter tissue intensity file

wm_prior_file: white matter tissue intensity file

csf_prior_file: csf tissue intensity file

arguments:

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

name: pipeline name (default = “segment_atropos_pipe”)

Outputs:

threshold_csf.out_file:

csf tissue intensity mask in subject space

threshold_gm.out_file:

grey matter tissue intensity mask in subject space

threshold_wm.out_file:

white matter tissue intensity mask in subject space