API Documentation¶

Pipelines¶

Full pipelines (macapype.pipelines.full_pipelines):

SPM based:

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

ANTS based:

`create_full_ants_subpipes`	Description: Segment T1 (using T2 for bias correction) .
`create_full_T1_ants_subpipes`	Description: Full pipeline to segment T1 (with no T2).

*ANTS based (intermediate pipelines)

`create_brain_extraction_pipe`	Description: Brain extraction with atlas-brex after debiasing
`create_brain_segment_from_mask_pipe`	Description: Segment T1 (using T2 for bias correction) and a previously computed mask with NMT Atlas and atropos segment.
`create_brain_extraction_T1_pipe`	Description: Brain extraction with only T1 images.
`create_brain_segment_from_mask_T1_pipe`	Description: Segment T1 from a previously computed mask.

Data preparation (macapype.pipelines.prepare):

`create_short_preparation_pipe`	Description: short data preparation (average, reorient, crop/betcrop and denoise)
`create_short_preparation_T1_pipe`	Description: T1 only short preparation
`create_long_single_preparation_pipe`	Description: Long data preparation, T1s and T2s are averaged (by modality) and then average imgs are processed.
`create_long_multi_preparation_pipe`	Description: Long data preparation, each T1 and T2 is processed independantly (mapnode).

(hidden)

`_create_prep_pipeline`	Description: hidden function for sequence of preprocessing
`_create_mapnode_prep_pipeline`	Description: hidden function for sequence of preprocessing (mapnode)

Correct bias (macapype.pipelines.correct_bias):

`create_correct_bias_pipe`	Description: Correct bias using T1 and T2 images
`create_masked_correct_bias_pipe`	Description: Correct bias using T1 and T2 images in a mask

Register (macapype.pipelines.register):

Description: Register template to anat with the script NMT_subject_align

Brain extraction (macapype.pipelines.extract_brain):

`create_extract_pipe`	Description: Extract T1 brain using AtlasBrex
`create_extract_T1_pipe`	Description: Extract T1 brain using AtlasBrex

Segment (macapype.pipelines.segment):

`create_old_segment_pipe`	Description: Extract brain using tissues masks output by SPM's old_segment
`create_segment_atropos_pipe`	Description: Segmentation with ANTS atropos script

Surface (macapype.pipelines.surface):

`create_nii_to_mesh_pipe`	Description: basic nii to mesh pipeline after segmentation
`create_nii_to_mesh_fs_pipe`	Description: surface generation using freesurfer tools

(hidden)

Description: Split segmentated tissus according hemisheres after removal of cortical structure

Surface (macapype.nodes.surface):

Definition: Create a Gifti mesh from a binary Nifti image

Segment (macapype.nodes.segment):

Description: Wrap of antsAtroposN4.sh

Extract brain (macapype.nodes.extract_brain):

`T1xT2BET`	Description: Brain extraction using T1 and T2 images
`AtlasBREX`	Description: Atlas based BrainExtraction

Correct bias (macapype.nodes.correct_bias):

Description: Bias field correction using T1w & T2w images.

Register (macapype.nodes.register):

`IterREGBET`	Description: Iterative registration of the in-file to the ref file ( registered brain mask of the ref image is used at each iteration).
`NMTSubjectAlign`	Description: Align NMT subject to template (NMT 1.2)
`NMTSubjectAlign2`	Description: Align NMT subject to template (NMT 1.3)

Prepare (macapype.nodes.prepare):

Description: Crop image(s) based on a brain extraction.

Utils tests (macapype.utils.utils_tests):

Load test data, template and needed scripts