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Add defacing to docs #98

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Nov 27, 2024
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4 changes: 4 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand All @@ -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",
)
]

Expand Down
16 changes: 16 additions & 0 deletions docs/source/defacing.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
defacing
============================================



defacing.defacer
--------------------------------------------

.. automodule:: brainles_preprocessing.defacing.defacer


defacing.quickshear
--------------------------------------

.. automodule:: brainles_preprocessing.defacing.quickshear.quickshear

6 changes: 6 additions & 0 deletions docs/source/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -41,3 +41,9 @@ Indices and tables
:caption: registration:

registration.rst

.. toctree::
:maxdepth: 2
:caption: defacing:

defacing.rst