diff --git a/README.md b/README.md index 61d23c8..475e18e 100644 --- a/README.md +++ b/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/) diff --git a/docs/source/brainles-preprocessing.rst b/docs/source/brainles-preprocessing.rst index 11a7019..67c1006 100644 --- a/docs/source/brainles-preprocessing.rst +++ b/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 + diff --git a/docs/source/index.rst b/docs/source/index.rst index 4f7bee8..6c20d97 100644 --- a/docs/source/index.rst +++ b/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: diff --git a/docs/source/n4-bias-correction.rst b/docs/source/n4-bias-correction.rst new file mode 100644 index 0000000..7e54b7b --- /dev/null +++ b/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 +