diff --git a/brainles_preprocessing/modality.py b/brainles_preprocessing/modality.py
index 918bc2e..fca3219 100644
--- a/brainles_preprocessing/modality.py
+++ b/brainles_preprocessing/modality.py
@@ -42,19 +42,49 @@ def __init__(
         self,
         modality_name: str,
         input_path: str,
-        output_path: str,
-        bet: bool,
-        atlas_correction: bool = True,
+        raw_bet_output_path: str = None,
+        raw_skull_output_path: str = None,
+        normalized_bet_output_path: str = None,
+        normalized_skull_output_path: str = None,
         normalizer: Optional[Normalizer] = None,
+        atlas_correction: bool = True,
     ) -> None:
         self.modality_name = modality_name
         self.input_path = turbopath(input_path)
-        self.output_path = turbopath(output_path)
-        self.bet = bet
-        self.atlas_correction = atlas_correction
+        if (
+            raw_bet_output_path is None
+            and normalized_bet_output_path is None
+            and raw_skull_output_path is None
+            and normalized_skull_output_path is None
+        ):
+            raise ValueError(
+                "All output paths are None. At least one output path must be provided."
+            )
+        self.raw_bet_output_path = turbopath(raw_bet_output_path)
+        self.raw_skull_output_path = turbopath(raw_skull_output_path)
+        if normalized_bet_output_path is not None:
+            if normalizer is None:
+                raise ValueError(
+                    "A normalizer must be provided if normalized_bet_output_path is not None."
+                )
+        self.normalized_bet_output_path = turbopath(normalized_bet_output_path)
+
+        if normalized_skull_output_path is not None:
+            if normalizer is None:
+                raise ValueError(
+                    "A normalizer must be provided if normalized_skull_output_path is not None."
+                )
+        self.normalized_skull_output_path = turbopath(normalized_skull_output_path)
+
         self.normalizer = normalizer
+        self.atlas_correction = atlas_correction
+
         self.current = self.input_path
 
+    @property
+    def bet(self) -> bool:
+        return any([self.raw_bet_output_path, self.normalized_bet_output_path])
+
     def normalize(
         self,
         temporary_directory: str,
@@ -225,3 +255,24 @@ def extract_brain_region(
         if self.bet is True:
             self.current = atlas_bet_cm
         return atlas_mask_path
+
+    def save_current_image(
+        self,
+        output_path: str,
+        normalization=False,
+    ) -> None:
+        os.makedirs(output_path.parent, exist_ok=True)
+
+        if normalization is False:
+            shutil.copyfile(
+                self.current,
+                output_path,
+            )
+        elif normalization is True:
+            image = read_nifti(self.current)
+            normalized_image = self.normalizer.normalize(image=image)
+            write_nifti(
+                input_array=normalized_image,
+                output_nifti_path=output_path,
+                reference_nifti_path=self.current,
+            )
diff --git a/brainles_preprocessing/preprocessor.py b/brainles_preprocessing/preprocessor.py
index 17f7a46..e03d588 100644
--- a/brainles_preprocessing/preprocessor.py
+++ b/brainles_preprocessing/preprocessor.py
@@ -103,17 +103,25 @@ def run(
         save_dir_atlas_registration: Optional[str] = None,
         save_dir_atlas_correction: Optional[str] = None,
         save_dir_brain_extraction: Optional[str] = None,
-        save_dir_unnormalized: Optional[str] = None,
     ):
         """
-        Execute the preprocessing pipeline.
+        Execute the preprocessing pipeline, encompassing coregistration, atlas-based registration,
+        atlas correction, and optional brain extraction.
 
         Args:
             save_dir_coregistration (str, optional): Directory path to save coregistration results.
             save_dir_atlas_registration (str, optional): Directory path to save atlas registration results.
             save_dir_atlas_correction (str, optional): Directory path to save atlas correction results.
             save_dir_brain_extraction (str, optional): Directory path to save brain extraction results.
-            save_dir_unnormalized (str, optional): Directory path to save unnormalized images.
+
+        This method orchestrates the entire preprocessing workflow by sequentially performing:
+
+        1. Coregistration: Aligning moving modalities to the central modality.
+        2. Atlas Registration: Aligning the central modality to a predefined atlas.
+        3. Atlas Correction: Applying additional correction in atlas space if specified.
+        4. Brain Extraction: Optionally extracting brain regions using specified masks.
+
+        Results are saved in the specified directories, allowing for modular and configurable output storage.
         """
         # Coregister moving modalities to center modality
         coregistration_dir = os.path.join(self.temp_folder, "coregistration")
@@ -142,22 +150,22 @@ def run(
         )
 
         # Register center modality to atlas
-        file_name = f"atlas__{self.center_modality.modality_name}"
+        center_file_name = f"atlas__{self.center_modality.modality_name}"
         transformation_matrix = self.center_modality.register(
             registrator=self.registrator,
             fixed_image_path=self.atlas_image_path,
             registration_dir=self.atlas_dir,
-            moving_image_name=file_name,
+            moving_image_name=center_file_name,
         )
 
         # Transform moving modalities to atlas
         for moving_modality in self.moving_modalities:
-            file_name = f"atlas__{moving_modality.modality_name}"
+            moving_file_name = f"atlas__{moving_modality.modality_name}"
             moving_modality.transform(
                 registrator=self.registrator,
                 fixed_image_path=self.atlas_image_path,
                 registration_dir_path=self.atlas_dir,
-                moving_image_name=file_name,
+                moving_image_name=moving_file_name,
                 transformation_matrix_path=transformation_matrix,
             )
         self._save_output(
@@ -171,12 +179,12 @@ def run(
 
         for moving_modality in self.moving_modalities:
             if moving_modality.atlas_correction is True:
-                file_name = f"atlas_corrected__{self.center_modality.modality_name}__{moving_modality.modality_name}"
+                moving_file_name = f"atlas_corrected__{self.center_modality.modality_name}__{moving_modality.modality_name}"
                 moving_modality.register(
                     registrator=self.registrator,
                     fixed_image_path=self.center_modality.current,
                     registration_dir=atlas_correction_dir,
-                    moving_image_name=file_name,
+                    moving_image_name=moving_file_name,
                 )
 
         if self.center_modality.atlas_correction is True:
@@ -193,8 +201,22 @@ def run(
             save_dir=save_dir_atlas_correction,
         )
 
+        # now we save images that are not skullstripped
+        for modality in self.all_modalities:
+            if modality.raw_skull_output_path:
+                modality.save_current_image(
+                    modality.raw_skull_output_path,
+                    normalization=False,
+                )
+            if modality.normalized_skull_output_path:
+                modality.save_current_image(
+                    modality.normalized_skull_output_path,
+                    normalization=True,
+                )
+
         # Optional: Brain extraction
         brain_extraction = any(modality.bet for modality in self.all_modalities)
+
         if brain_extraction:
             bet_dir = os.path.join(self.temp_folder, "brain-extraction")
             os.makedirs(bet_dir, exist_ok=True)
@@ -216,21 +238,18 @@ def run(
                 save_dir=save_dir_brain_extraction,
             )
 
-        # Optional: Normalization
-        normalization = any(modality.normalizer for modality in self.all_modalities)
-        if normalization:
-            for modality in [self.center_modality] + self.moving_modalities:
-                modality.normalize(
-                    temporary_directory=self.temp_folder,
-                    store_unnormalized=save_dir_unnormalized,
-                )
-
+        # now we save images that are skullstripped
         for modality in self.all_modalities:
-            os.makedirs(modality.output_path.parent, exist_ok=True)
-            shutil.copyfile(
-                modality.current,
-                modality.output_path,
-            )
+            if modality.raw_bet_output_path:
+                modality.save_current_image(
+                    modality.raw_bet_output_path,
+                    normalization=False,
+                )
+            if modality.normalized_bet_output_path:
+                modality.save_current_image(
+                    modality.normalized_bet_output_path,
+                    normalization=True,
+                )
 
     def _save_output(
         self,
diff --git a/example_data/OtherEXampleFromTCIA/MRHR_FLAIR_AX_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_FLAIR_AX_SE_IR_5_tir2d1_21_fla.nii.gz b/example/example_data/OtherEXampleFromTCIA/MRHR_FLAIR_AX_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_FLAIR_AX_SE_IR_5_tir2d1_21_fla.nii.gz
similarity index 100%
rename from example_data/OtherEXampleFromTCIA/MRHR_FLAIR_AX_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_FLAIR_AX_SE_IR_5_tir2d1_21_fla.nii.gz
rename to example/example_data/OtherEXampleFromTCIA/MRHR_FLAIR_AX_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_FLAIR_AX_SE_IR_5_tir2d1_21_fla.nii.gz
diff --git a/example_data/OtherEXampleFromTCIA/MRHR_T1_AX_POST_GAD_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_T1_AX_POST_GAD_SE_13_se2d1r_t1c.nii.gz b/example/example_data/OtherEXampleFromTCIA/MRHR_T1_AX_POST_GAD_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_T1_AX_POST_GAD_SE_13_se2d1r_t1c.nii.gz
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rename to example/example_data/OtherEXampleFromTCIA/MRHR_T1_AX_POST_GAD_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_T1_AX_POST_GAD_SE_13_se2d1r_t1c.nii.gz
diff --git a/example_data/OtherEXampleFromTCIA/MRHR_T2_AX_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_T2_AX_SE_2_tse2d1_11_t2.nii.gz b/example/example_data/OtherEXampleFromTCIA/MRHR_T2_AX_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_T2_AX_SE_2_tse2d1_11_t2.nii.gz
similarity index 100%
rename from example_data/OtherEXampleFromTCIA/MRHR_T2_AX_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_T2_AX_SE_2_tse2d1_11_t2.nii.gz
rename to example/example_data/OtherEXampleFromTCIA/MRHR_T2_AX_OtherEXampleTCIA_TCGA-FG-6692_Si_TCGA-FG-6692_MRHR_T2_AX_SE_2_tse2d1_11_t2.nii.gz
diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c.nii.gz
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rename from example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c.nii.gz
rename to example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c.nii.gz
diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__flair.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__flair.nii.gz
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rename from example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__flair.nii.gz
rename to example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__flair.nii.gz
diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__flair.txt b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__flair.txt
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__t1.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__t1.nii.gz
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rename to example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__t1.nii.gz
diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__t1.txt b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__t1.txt
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rename to example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__t1.txt
diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__t2.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__t2.nii.gz
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__t2.txt b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-correction/atlas_corrected__t1c__t2.txt
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__flair.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__flair.nii.gz
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__t1.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__t1.nii.gz
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__t1c.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__t1c.nii.gz
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__t1c.txt b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__t1c.txt
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__t2.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__t2.nii.gz
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/atlas_bet_t1c.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/atlas_bet_t1c.nii.gz
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/atlas_bet_t1c_mask.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/atlas_bet_t1c_mask.nii.gz
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__flair.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__flair.nii.gz
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__t2.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__t2.nii.gz
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__flair.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__flair.nii.gz
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__flair.txt b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__flair.txt
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rename from example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__flair.txt
rename to example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__flair.txt
diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__t1.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__t1.nii.gz
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__t1.txt b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__t1.txt
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diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__t2.nii.gz b/example/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__t2.nii.gz
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diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/atlas_corrected__t1c__t2.nii.gz b/example/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/raw_skull/TCGA-DU-7294_t2_skull_raw.nii.gz
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diff --git a/example_modality_centric_preprocessor.py b/example/example_modality_centric_preprocessor.py
similarity index 62%
rename from example_modality_centric_preprocessor.py
rename to example/example_modality_centric_preprocessor.py
index 9fca4bc..de75c36 100644
--- a/example_modality_centric_preprocessor.py
+++ b/example/example_modality_centric_preprocessor.py
@@ -22,7 +22,10 @@ def preprocess(inputDir):
 
         # is the exam already processed?
         brainles_dir = turbopath(inputDir) + "/" + inputDir.name + "_brainles"
-        prep_dir = brainles_dir + "/preprocessed"
+        raw_bet_dir = brainles_dir / "raw_bet"
+        norm_bet_dir = brainles_dir / "normalized_bet"
+        raw_skull_dir = brainles_dir / "raw_skull"
+        norm_skull_dir = brainles_dir / "normalized_skull"
 
         # if not os.path.exists(prep_dir):
         # if os.path.exists(prep_dir):
@@ -54,8 +57,13 @@ def preprocess(inputDir):
             center = Modality(
                 modality_name="t1c",
                 input_path=t1cFile,
-                output_path=prep_dir + "/" + inputDir.name + "_t1c.nii.gz",
-                bet=False,
+                raw_bet_output_path=raw_bet_dir / inputDir.name + "_t1c_bet_raw.nii.gz",
+                raw_skull_output_path=raw_skull_dir / inputDir.name
+                + "_t1c_skull_raw.nii.gz",
+                normalized_bet_output_path=norm_bet_dir / inputDir.name
+                + "_t1c_bet_normalized.nii.gz",
+                normalized_skull_output_path=norm_skull_dir / inputDir.name
+                + "_t1c_skull_normalized.nii.gz",
                 atlas_correction=True,
                 normalizer=percentile_normalizer,
             )
@@ -64,27 +72,42 @@ def preprocess(inputDir):
                 Modality(
                     modality_name="t1",
                     input_path=t1File,
-                    output_path=prep_dir + "/" + inputDir.name + "_t1.nii.gz",
-                    # raw_brainextracted_output_path,
-                    # normalized_brainextracted_output_path,
-                    # raw_withskull_output_path,
-                    # normalized_withskull_output_path,
+                    raw_bet_output_path=raw_bet_dir / inputDir.name
+                    + "_t1_bet_raw.nii.gz",
+                    raw_skull_output_path=raw_skull_dir / inputDir.name
+                    + "_t1_skull_raw.nii.gz",
+                    normalized_bet_output_path=norm_bet_dir / inputDir.name
+                    + "_t1_bet_normalized.nii.gz",
+                    normalized_skull_output_path=norm_skull_dir / inputDir.name
+                    + "_t1_skull_normalized.nii.gz",
                     atlas_correction=True,
                     normalizer=percentile_normalizer,
                 ),
                 Modality(
                     modality_name="t2",
                     input_path=t2File,
-                    output_path=prep_dir + "/" + inputDir.name + "_t2.nii.gz",
-                    bet=True,
+                    raw_bet_output_path=raw_bet_dir / inputDir.name
+                    + "_t2_bet_raw.nii.gz",
+                    raw_skull_output_path=raw_skull_dir / inputDir.name
+                    + "_t2_skull_raw.nii.gz",
+                    normalized_bet_output_path=norm_bet_dir / inputDir.name
+                    + "_t2_bet_normalized.nii.gz",
+                    normalized_skull_output_path=norm_skull_dir / inputDir.name
+                    + "_t2_skull_normalized.nii.gz",
                     atlas_correction=True,
                     normalizer=percentile_normalizer,
                 ),
                 Modality(
                     modality_name="flair",
                     input_path=flaFile,
-                    output_path=prep_dir + "/" + inputDir.name + "_fla.nii.gz",
-                    bet=True,
+                    raw_bet_output_path=raw_bet_dir / inputDir.name
+                    + "_fla_bet_raw.nii.gz",
+                    raw_skull_output_path=raw_skull_dir / inputDir.name
+                    + "_fla_skull_raw.nii.gz",
+                    normalized_bet_output_path=norm_bet_dir / inputDir.name
+                    + "_fla_bet_normalized.nii.gz",
+                    normalized_skull_output_path=norm_skull_dir / inputDir.name
+                    + "_fla_skull_normalized.nii.gz",
                     atlas_correction=True,
                     normalizer=percentile_normalizer,
                 ),
@@ -104,7 +127,6 @@ 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_unnormalized=brainles_dir + "/unnormalized",
             )
 
     except Exception as e:
@@ -118,7 +140,7 @@ def preprocess(inputDir):
 
 ### *** GOGOGO *** ###
 if __name__ == "__main__":
-    EXAMPLE_DATA_DIR = turbopath("example_data")
+    EXAMPLE_DATA_DIR = turbopath("example/example_data")
 
     exams = EXAMPLE_DATA_DIR.dirs()
 
diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/atlas_corrected__t1c__flair.txt b/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/atlas_corrected__t1c__flair.txt
deleted file mode 100644
index b045cb2..0000000
--- a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/atlas_corrected__t1c__flair.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-0.9999986 0.0004745152 0.001594621 -0.2643708
--0.0004719235 0.9999986 -0.001640065 -0.2377842
--0.001595397 0.001639307 0.9999974 -0.3903068
-0 0 0 1
diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/atlas_corrected__t1c__t1.txt b/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/atlas_corrected__t1c__t1.txt
deleted file mode 100644
index d17faa9..0000000
--- a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/atlas_corrected__t1c__t1.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-0.9999967 -0.002466233 -0.0006566526 0.2820461
-0.002466184 0.999997 -3.481855e-05 0.3856321
-0.0006567395 3.319529e-05 0.9999998 0.2829154
-0 0 0 1
diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/atlas_corrected__t1c__t2.txt b/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/atlas_corrected__t1c__t2.txt
deleted file mode 100644
index 1a4fb67..0000000
--- a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/atlas_corrected__t1c__t2.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-0.9999985 -0.0004714925 0.001716384 -0.1140093
-0.0004710982 0.9999999 0.0002239809 0.02963747
--0.001716489 -0.0002231678 0.9999985 -0.2469956
-0 0 0 1
diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__fla.nii.gz b/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__fla.nii.gz
deleted file mode 100644
index 2e2bf28..0000000
Binary files a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__fla.nii.gz and /dev/null differ
diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__fla.nii.gz b/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__fla.nii.gz
deleted file mode 100644
index 1f34d44..0000000
Binary files a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__fla.nii.gz and /dev/null differ
diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__fla.txt b/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__fla.txt
deleted file mode 100644
index d312371..0000000
--- a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__fla.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-0.9996052 0.008290411 -0.02684693 0.4557816
--0.008523657 0.9999268 -0.008585239 1.334237
-0.02677379 0.008810687 0.9996027 -1.209411
-0 0 0 1
diff --git a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/unnormalized/unnormalized__fla.nii.gz b/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/unnormalized/unnormalized__fla.nii.gz
deleted file mode 100644
index e1715e9..0000000
Binary files a/example_data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/unnormalized/unnormalized__fla.nii.gz and /dev/null differ
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/atlas_corrected__t1c__flair.txt b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/atlas_corrected__t1c__flair.txt
deleted file mode 100644
index c42602c..0000000
--- a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/atlas_corrected__t1c__flair.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-0.9999974 0.000648056 -0.002159797 0.04889112
--0.000650483 0.9999992 -0.00112357 -0.003959787
-0.002159069 0.001124969 0.999997 0.04360351
-0 0 0 1
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/atlas_corrected__t1c__t1.txt b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/atlas_corrected__t1c__t1.txt
deleted file mode 100644
index 190fa04..0000000
--- a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/atlas_corrected__t1c__t1.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-0.9999996 -0.0008996009 0.0001597377 0.1239718
-0.0008998092 0.9999989 -0.001229477 0.25916
--0.0001586301 0.001229625 0.9999993 -0.1732138
-0 0 0 1
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/atlas_corrected__t1c__t2.txt b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/atlas_corrected__t1c__t2.txt
deleted file mode 100644
index fd01b1d..0000000
--- a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/atlas_corrected__t1c__t2.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-0.9999991 0.000149987 0.001336964 -0.03884844
--0.0001501937 1 0.0001575474 0.0593403
--0.001336942 -0.0001577501 0.9999991 -0.04306287
-0 0 0 1
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/brain_masked/brain_masked__fla.nii.gz b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/brain_masked/brain_masked__fla.nii.gz
deleted file mode 100644
index 2e2bf28..0000000
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diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/co-registration/co__t1c__fla.nii.gz b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/co-registration/co__t1c__fla.nii.gz
deleted file mode 100644
index 1f34d44..0000000
Binary files a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/co-registration/co__t1c__fla.nii.gz and /dev/null differ
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/co-registration/co__t1c__fla.txt b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/co-registration/co__t1c__fla.txt
deleted file mode 100644
index d312371..0000000
--- a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/co-registration/co__t1c__fla.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-0.9996052 0.008290411 -0.02684693 0.4557816
--0.008523657 0.9999268 -0.008585239 1.334237
-0.02677379 0.008810687 0.9996027 -1.209411
-0 0 0 1
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/unnormalized/unnormalized__fla.nii.gz b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/unnormalized/unnormalized__fla.nii.gz
deleted file mode 100644
index 554eb16..0000000
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