diff --git a/README.md b/README.md index d5363c5..39aa327 100644 --- a/README.md +++ b/README.md @@ -54,8 +54,10 @@ center = CenterModality( # specify the output paths for the raw and normalized images of each step - here only for atlas registered and brain extraction raw_skull_output_path="patient/raw_skull_dir/t1c_skull_raw.nii.gz", raw_bet_output_path="patient/raw_bet_dir/t1c_bet_raw.nii.gz", + raw_defaced_output_path="patient/raw_defaced_dir/t1c_defaced_raw.nii.gz", normalized_skull_output_path="patient/norm_skull_dir/t1c_skull_normalized.nii.gz", normalized_bet_output_path="patient/norm_bet_dir/t1c_bet_normalized.nii.gz", + normalized_defaced_output_path="patient/norm_defaced_dir/t1c_defaced_normalized.nii.gz", # specify output paths for the brain extraction and defacing masks bet_mask_output_path="patient/masks/t1c_bet_mask.nii.gz", defacing_mask_output_path="patient/masks/t1c_defacing_mask.nii.gz", @@ -69,8 +71,10 @@ moving_modalities = [ # specify the output paths for the raw and normalized images of each step - here only for atlas registered and brain extraction raw_skull_output_path="patient/raw_skull_dir/fla_skull_raw.nii.gz", raw_bet_output_path="patient/raw_bet_dir/fla_bet_raw.nii.gz", + raw_defaced_output_path="patient/raw_defaced_dir/fla_defaced_raw.nii.gz", normalized_skull_output_path="patient/norm_skull_dir/fla_skull_normalized.nii.gz", normalized_bet_output_path="patient/norm_bet_dir/fla_bet_normalized.nii.gz", + normalized_defaced_output_path="patient/norm_defaced_dir/fla_defaced_normalized.nii.gz", ) ] diff --git a/docs/source/defacing.rst b/docs/source/defacing.rst new file mode 100644 index 0000000..7b6baa3 --- /dev/null +++ b/docs/source/defacing.rst @@ -0,0 +1,16 @@ +defacing +============================================ + + + +defacing.defacer +-------------------------------------------- + +.. automodule:: brainles_preprocessing.defacing.defacer + + +defacing.quickshear +-------------------------------------- + +.. automodule:: brainles_preprocessing.defacing.quickshear.quickshear + diff --git a/docs/source/index.rst b/docs/source/index.rst index 0d094bd..4f7bee8 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -41,3 +41,9 @@ Indices and tables :caption: registration: registration.rst + +.. toctree:: + :maxdepth: 2 + :caption: defacing: + + defacing.rst