macapype.pipelines.segment.create_old_segment_pipe

macapype.pipelines.segment.create_old_segment_pipe(params_template, params={}, name='old_segment_pipe')

Description: Extract brain using tissues masks output by SPM’s old_segment

Function:

• Segment the T1 using given priors;

• Threshold GM, WM and CSF maps;

Params:

• segment (see Segment)

• threshold_gm, threshold_wm, threshold_csf (see Threshold for arguments) - also available as indiv_params

• dilate_mask (see DilateMask)

• erode_mask (see ErodeMask)

Inputs:

inputnode:

T1: T1 file name

arguments:

priors: list of file names

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

name: pipeline name (default = “old_segment_pipe”)

Outputs:

fill_holes.out_file:

filled mask after erode

fill_holes_dil.out_file

filled mask after dilate

threshold_gm, threshold_wm, threshold_csf.out_file:

resp grey matter, white matter, and csf after thresholding