macapype.pipelines.full_pipelines.create_full_spm_subpipes

macapype.pipelines.full_pipelines.create_full_spm_subpipes(params_template, params={}, name='full_spm_subpipes', pad=False, space='template')

Description: SPM based segmentation pipeline from T1w and T2w images in template space

Processing steps:

• Data preparation (short, with betcrop or crop)

• debias using T1xT2BiasFieldCorrection (using mask is betcrop)

• registration to template file with IterREGBET

• SPM segmentation the old way (SPM8, not dartel based)

Params:

• short_data_preparation_pipe (see create_short_preparation_pipe)

• debias (see T1xT2BiasFieldCorrection) - also available as indiv_params

• reg (see IterREGBET) - also available as indiv_params

• native_old_segment_pipe (see create_native_old_segment_pipe)

Inputs:

inputnode:

list_T1:

T1 file names

list_T2:

T2 file names

indiv_params (opt):

dict with individuals parameters for some nodes

arguments:

params_template:

dict of template files containing brain_template and priors (list of template based segmented tissues)

params:

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

name:

pipeline name (default = “full_spm_subpipes”)

Outputs:

old_segment_pipe.thresh_gm.out_file:

segmented grey matter in template space

old_segment_pipe.thresh_wm.out_file:

segmented white matter in template space

old_segment_pipe.thresh_csf.out_file:

segmented csf in template space