macapype.pipelines.surface.create_nii_to_mesh_pipe¶

macapype.pipelines.surface.create_nii_to_mesh_pipe(params, params_template, name='nii_to_mesh_pipe')[source]¶

Description: basic nii to mesh pipeline after segmentation

Processing steps:

split in hemisphere after removal of the subcortical structures
using scipy marching cube methods to compute mesh
some smoothing (using brain-slam)

Params:

split_hemi_pipe (see _create_split_hemi_pipe for arguments)

mesh_L_GM, mesh_R_GM, mesh_L_WM, mesh_R_WM (see Meshify for arguments)

Inputs:

inputnode:

warpinv_file:
non-linear transformation (from NMT_subject_align)

inv_transfo_file:
inverse transformation

aff_file:
affine transformation file

t1_ref_file:
preprocessd T1

segmented_file:
from atropos segmentation, with all the tissues segmented

arguments:

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

name:
pipeline name (default = “nii_to_mesh_pipe”)

Outputs: