Corrected QuickshearDefacer argument name mismatch

BrainLesion · Oct 31, 2024 · 0a8a2b4 · 0a8a2b4
1 parent 36be733
commit 0a8a2b4
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Showing 2 changed files with 20 additions and 1 deletion.
diff --git a/brainles_preprocessing/modality.py b/brainles_preprocessing/modality.py
@@ -401,7 +401,7 @@ def deface(
 
             defacer.deface(
                 mask_image_path=atlas_mask_path,
-                bet_img_path=self.steps[PreprocessorSteps.BET],
+                input_image_path=self.steps[PreprocessorSteps.BET],
             )
             return atlas_mask_path
         else:

diff --git a/example/example_modality_centric_preprocessor.py b/example/example_modality_centric_preprocessor.py
@@ -26,6 +26,8 @@ def preprocess(inputDir):
     norm_bet_dir = brainles_dir / "normalized_bet"
     raw_skull_dir = brainles_dir / "raw_skull"
     norm_skull_dir = brainles_dir / "normalized_skull"
+    raw_deface_dir = brainles_dir / "raw_defaced"
+    norm_deface_dir = brainles_dir / "normalized_defaced"
 
     t1_file = inputDir.files("*t1.nii.gz")
     t1c_file = inputDir.files("*t1c.nii.gz")
@@ -58,6 +60,10 @@ def preprocess(inputDir):
             + "_t1c_bet_normalized.nii.gz",
             normalized_skull_output_path=norm_skull_dir / inputDir.name
             + "_t1c_skull_normalized.nii.gz",
+            raw_defaced_output_path=raw_deface_dir / inputDir.name
+            + "_t1c_defaced_raw.nii.gz",
+            normalized_defaced_output_path=norm_deface_dir
+            / "_t1c_defaced_normalized.nii.gz",
             atlas_correction=True,
             normalizer=percentile_normalizer,
         )
@@ -72,6 +78,10 @@ def preprocess(inputDir):
                 + "_t1_bet_normalized.nii.gz",
                 normalized_skull_output_path=norm_skull_dir / inputDir.name
                 + "_t1_skull_normalized.nii.gz",
+                raw_defaced_output_path=raw_deface_dir / inputDir.name
+                + "_t1_defaced_raw.nii.gz",
+                normalized_defaced_output_path=norm_deface_dir / inputDir.name
+                + "_t1_defaced_normalized.nii.gz",
                 atlas_correction=True,
                 normalizer=percentile_normalizer,
             ),
@@ -85,6 +95,10 @@ def preprocess(inputDir):
                 + "_t2_bet_normalized.nii.gz",
                 normalized_skull_output_path=norm_skull_dir / inputDir.name
                 + "_t2_skull_normalized.nii.gz",
+                raw_defaced_output_path=raw_deface_dir / inputDir.name
+                + "_t2_defaced_raw.nii.gz",
+                normalized_defaced_output_path=norm_deface_dir / inputDir.name
+                + "_t2_defaced_normalized.nii.gz",
                 atlas_correction=True,
                 normalizer=percentile_normalizer,
             ),
@@ -98,6 +112,10 @@ def preprocess(inputDir):
                 + "_fla_bet_normalized.nii.gz",
                 normalized_skull_output_path=norm_skull_dir / inputDir.name
                 + "_fla_skull_normalized.nii.gz",
+                raw_defaced_output_path=raw_deface_dir / inputDir.name
+                + "_flair_defaced_raw.nii.gz",
+                normalized_defaced_output_path=norm_deface_dir / inputDir.name
+                + "_flair_defaced_normalized.nii.gz",
                 atlas_correction=True,
                 normalizer=percentile_normalizer,
             ),
@@ -120,6 +138,7 @@ def preprocess(inputDir):
             save_dir_atlas_registration=brainles_dir + "/atlas-registration",
             save_dir_atlas_correction=brainles_dir + "/atlas-correction",
             save_dir_brain_extraction=brainles_dir + "/brain-extraction",
+            save_dir_defacing=brainles_dir + "/defacing",
         )