doc: state that the workflow is not a nipype version of ``antsBrainExtraction``
@@ -61,20 +61,31 @@ def init_brain_extraction_wf(
"""
Build a workflow for atlas-based brain extraction on anatomical MRI data.
- A Nipype implementation of the official ANTs' ``antsBrainExtraction.sh``
- workflow (only for 3D images).
+ This is a Nipype implementation of atlas-based brain extraction inspired by
+ the official ANTs' ``antsBrainExtraction.sh`` workflow (only for 3D images).
- The official workflow is built as follows (and this implementation
- follows the same organization):
+ The workflow follows the following structure:
- 1. Step 1 performs several clerical tasks (adding padding, calculating
- the Laplacian of inputs, affine initialization) and the core
- spatial normalization.
+ 1. Step 1 performs several clerical tasks (preliminary INU correction,
+ calculating the Laplacian of inputs, affine initialization) and the
+ core spatial normalization.
2. Maps the brain mask into target space using the normalization
calculated in 1.
- 3. Superstep 1b: smart binarization of the brain mask
- 4. Superstep 6: apply ATROPOS and massage its outputs
- 5. Superstep 7: use results from 4 to refine the brain mask
+ 3. Superstep 1b: binarization of the brain mask
+ 4. Maps the WM probability map from the template, if such prior exists.
+ Combines the BS (brainstem) probability map before mapping if the WM
+ and BS are given separately (as it is the case for ``OASIS30ANTs``.)
+ 5. Run a second N4 INU correction round, using the prior mapped into
+ individual step in step 4.
+ 6. Superstep 6: apply ATROPOS on the INU-corrected result of step 5, and
+ massage its outputs
+ 7. Superstep 7: use results from 4 to refine the brain mask
+ 8. If exist, use priors from step 4, calculate the overlap of the posteriors
+ estimated in step 4 to select that overlapping the most with the WM+BS
+ prior from the template. Combine that posterior with the refined brain
+ mask and pass it on to the next step.
+ 9. Apply a final N4 using the refined brain mask (or the map calculated in
+ step 8 if priors were found) as weights map for the algorithm.
Workflow Graph
.. workflow::
@@ -466,9 +477,11 @@ def init_atropos_wf(
"""
Create an ANTs' ATROPOS workflow for brain tissue segmentation.
- Implements supersteps 6 and 7 of ``antsBrainExtraction.sh``,
+ Re-interprets supersteps 6 and 7 of ``antsBrainExtraction.sh``,
which refine the mask previously computed with the spatial
normalization to the template.
+ The workflow also executes steps 8 and 9 of the brain extraction
+ workflow.
Workflow Graph
.. workflow::
