From 9f4fdbbfd9a454df597591412d06f0be168c6918 Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Mon, 21 Jul 2025 12:33:38 +0200 Subject: [PATCH 1/3] Update FAQ section --- README.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) 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/) From 959fe21af7ce64cce4c9ee2a357d3b8ee29975eb Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Mon, 21 Jul 2025 12:34:06 +0200 Subject: [PATCH 2/3] Add n4 bias section and update preprocessor info --- docs/source/brainles-preprocessing.rst | 12 +++++++++--- docs/source/index.rst | 7 +++++++ docs/source/n4-bias-correction.rst | 16 ++++++++++++++++ 3 files changed, 32 insertions(+), 3 deletions(-) create mode 100644 docs/source/n4-bias-correction.rst diff --git a/docs/source/brainles-preprocessing.rst b/docs/source/brainles-preprocessing.rst index 11a7019..f4f8fbf 100644 --- a/docs/source/brainles-preprocessing.rst +++ b/docs/source/brainles-preprocessing.rst @@ -2,15 +2,21 @@ 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 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 + From 9e9461e43a4ccd1da4737ecd48fdf22b60291d0b Mon Sep 17 00:00:00 2001 From: Marcel Rosier Date: Mon, 21 Jul 2025 12:37:10 +0200 Subject: [PATCH 3/3] Add constants and transform class --- docs/source/brainles-preprocessing.rst | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/source/brainles-preprocessing.rst b/docs/source/brainles-preprocessing.rst index f4f8fbf..67c1006 100644 --- a/docs/source/brainles-preprocessing.rst +++ b/docs/source/brainles-preprocessing.rst @@ -20,3 +20,12 @@ Preprocessor .. automodule:: brainles_preprocessing.preprocessor.native_space_preprocessor +Constants +-------------------------------------------- +.. automodule:: brainles_preprocessing.constants + + +Transform +-------------------------------------------- +.. automodule:: brainles_preprocessing.transform +