Merge pull request #148 from BrainLesion/137-feature-bring-rtd-page-up-to-date

137 feature bring rtd page up to date

Author: neuronflow

README.md

@@ -138,11 +138,17 @@ We provide a (WIP) documentation. Have a look [here](https://brainles-preprocess
 Please credit the authors by citing their work.
 
 ### Registration
-We currently provide support for [ANTs](https://github.com/ANTsX/ANTs) (default), [Niftyreg](https://github.com/KCL-BMEIS/niftyreg) (Linux).
+We currently provide support for [ANTs](https://github.com/ANTsX/ANTs) (default), [Niftyreg](https://github.com/KCL-BMEIS/niftyreg) (Linux). We also offer basic support for [greedy](https://greedy.readthedocs.io/en/latest/reference.html#greedy-usage) and [elastix](https://pypi.org/project/itk-elastix/0.13.0/).
 
 ### Atlas Reference
-We provide the SRI-24 atlas from this [publication](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2915788/).
-However, custom atlases in NIfTI format are supported.
+We provide a range of different atlases, namely:
+-  [SRI24](https://www.nitrc.org/frs/download.php/4502/sri24_anatomy_unstripped_nifti.zip) and its [skull-stripped version](https://www.nitrc.org/frs/download.php/4499/sri24_anatomy_nifti.zip)
+-  A slightly modified SRI24 atlas as found in the BraTS challenges (also with a skull-stripped version)
+-  MNI152: [MNI_ICBM_2009c_Nonlinear_Symmetric](https://nist.mni.mcgill.ca/icbm-152-nonlinear-atlases-2009/)
+-  A slightly modified MNI152 atlas as found in the BraTS challenge 
+
+We also support supplying a custom atlas in NIfTI format
+
 
 ### N4 Bias correction
 We currently provide support for N4 Bias correction based on [SimpleITK](https://simpleitk.org/)

docs/source/brainles-preprocessing.rst

@@ -2,15 +2,30 @@ brainles_preprocessing
 ============================================
 
 
-modality
+Modality
 --------------------------------------------
 
 .. automodule:: brainles_preprocessing.modality
 
 
-preprocessor
+Preprocessor
 --------------------------------------------
 
-.. automodule:: brainles_preprocessing.preprocessor
+.. automodule:: brainles_preprocessing.preprocessor.preprocessor
 
 
+.. automodule:: brainles_preprocessing.preprocessor.atlas_centric_preprocessor
+
+
+.. automodule:: brainles_preprocessing.preprocessor.native_space_preprocessor
+
+
+Constants
+--------------------------------------------
+.. automodule:: brainles_preprocessing.constants
+
+
+Transform
+--------------------------------------------
+.. automodule:: brainles_preprocessing.transform
+

docs/source/index.rst

@@ -29,6 +29,13 @@ Indices and tables
    brainles-preprocessing.rst
 
 
+.. toctree::
+   :maxdepth: 2
+   :caption: N4 Bias Correction:
+
+   n4-bias-correction.rst
+
+
 .. toctree::
    :maxdepth: 2
    :caption: brain_extraction:

docs/source/n4-bias-correction.rst

@@ -0,0 +1,16 @@
+N4 Bias Correction
+============================================
+
+
+
+n4_bias_correction.n4_bias_corrector
+--------------------------------------------
+
+.. automodule:: brainles_preprocessing.n4_bias_correction.n4_bias_corrector
+
+
+n4_bias_correction.sitk
+--------------------------------------
+
+.. automodule:: brainles_preprocessing.n4_bias_correction.sitk.sitk_n4_bias_corrector
+