Rerun pipeline with new params

BrainLesion · Nov 22, 2023 · 4c5b009 · 4c5b009
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Showing 32 changed files with 16 additions and 8 deletions.
diff --git a/...a/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__fla.nii.gz b/...a/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__fla.nii.gz
diff --git a/...OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__flair.nii.gz b/...OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/atlas-registration/atlas__flair.nii.gz
diff --git a/...TCIA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__fla.nii.gz b/...TCIA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__fla.nii.gz
diff --git a/...IA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__flair.nii.gz b/...IA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__flair.nii.gz
diff --git a/...mTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__t1.nii.gz b/...mTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__t1.nii.gz
diff --git a/...mTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__t2.nii.gz b/...mTCIA/OtherEXampleFromTCIA_brainles/brain-extraction/brain_masked/brain_masked__t2.nii.gz
diff --git a/...ta/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__fla.nii.gz b/...ta/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__fla.nii.gz
diff --git a/..._data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__fla.txt b/..._data/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__fla.txt
@@ -1,4 +1,4 @@
-0.9746826 0.1823958 0.1293272 2.006546
--0.1904442 0.980279 0.05276459 0.8591887
--0.1171527 -0.07605835 0.9901971 -12.93682
+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/.../OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__flair.nii.gz b/.../OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__flair.nii.gz
diff --git a/...ata/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__flair.txt b/...ata/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/co-registration/co__t1c__flair.txt
@@ -0,0 +1,4 @@
+0.9746826 0.1823958 0.1293272 2.006546
+-0.1904442 0.980279 0.05276459 0.8591887
+-0.1171527 -0.07605835 0.9901971 -12.93682
+0 0 0 1
diff --git a/...XampleFromTCIA/OtherEXampleFromTCIA_brainles/preprocessed/OtherEXampleFromTCIA_fla.nii.gz b/...XampleFromTCIA/OtherEXampleFromTCIA_brainles/preprocessed/OtherEXampleFromTCIA_fla.nii.gz
diff --git a/...EXampleFromTCIA/OtherEXampleFromTCIA_brainles/preprocessed/OtherEXampleFromTCIA_t1.nii.gz b/...EXampleFromTCIA/OtherEXampleFromTCIA_brainles/preprocessed/OtherEXampleFromTCIA_t1.nii.gz
diff --git a/...XampleFromTCIA/OtherEXampleFromTCIA_brainles/preprocessed/OtherEXampleFromTCIA_t1c.nii.gz b/...XampleFromTCIA/OtherEXampleFromTCIA_brainles/preprocessed/OtherEXampleFromTCIA_t1c.nii.gz
diff --git a/...EXampleFromTCIA/OtherEXampleFromTCIA_brainles/preprocessed/OtherEXampleFromTCIA_t2.nii.gz b/...EXampleFromTCIA/OtherEXampleFromTCIA_brainles/preprocessed/OtherEXampleFromTCIA_t2.nii.gz
diff --git a/...therEXampleFromTCIA/OtherEXampleFromTCIA_brainles/unnormalized/unnormalized__flair.nii.gz b/...therEXampleFromTCIA/OtherEXampleFromTCIA_brainles/unnormalized/unnormalized__flair.nii.gz
diff --git a/...a/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/unnormalized/unnormalized__t1.nii.gz b/...a/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/unnormalized/unnormalized__t1.nii.gz
diff --git a/...a/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/unnormalized/unnormalized__t2.nii.gz b/...a/OtherEXampleFromTCIA/OtherEXampleFromTCIA_brainles/unnormalized/unnormalized__t2.nii.gz
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/atlas-registration/atlas__flair.nii.gz b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/atlas-registration/atlas__flair.nii.gz
diff --git a/...TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/brain_masked/brain_masked__fla.nii.gz b/...TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/brain_masked/brain_masked__fla.nii.gz
diff --git a/...GA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/brain_masked/brain_masked__flair.nii.gz b/...GA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/brain_masked/brain_masked__flair.nii.gz
diff --git a/.../TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/brain_masked/brain_masked__t1.nii.gz b/.../TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/brain_masked/brain_masked__t1.nii.gz
diff --git a/.../TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/brain_masked/brain_masked__t2.nii.gz b/.../TCGA-DU-7294/TCGA-DU-7294_brainles/brain-extraction/brain_masked/brain_masked__t2.nii.gz
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/co-registration/co__t1c__flair.nii.gz b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/co-registration/co__t1c__flair.nii.gz
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/co-registration/co__t1c__flair.txt b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/co-registration/co__t1c__flair.txt
@@ -0,0 +1,4 @@
+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/preprocessed/TCGA-DU-7294_fla.nii.gz b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/preprocessed/TCGA-DU-7294_fla.nii.gz
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/preprocessed/TCGA-DU-7294_t1.nii.gz b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/preprocessed/TCGA-DU-7294_t1.nii.gz
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/preprocessed/TCGA-DU-7294_t1c.nii.gz b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/preprocessed/TCGA-DU-7294_t1c.nii.gz
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/preprocessed/TCGA-DU-7294_t2.nii.gz b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/preprocessed/TCGA-DU-7294_t2.nii.gz
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/unnormalized/unnormalized__flair.nii.gz b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/unnormalized/unnormalized__flair.nii.gz
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/unnormalized/unnormalized__t1.nii.gz b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/unnormalized/unnormalized__t1.nii.gz
diff --git a/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/unnormalized/unnormalized__t2.nii.gz b/example_data/TCGA-DU-7294/TCGA-DU-7294_brainles/unnormalized/unnormalized__t2.nii.gz
diff --git a/example_modality_centric_preprocessor.py b/example_modality_centric_preprocessor.py
@@ -43,8 +43,8 @@ def preprocess(inputDir):
 
             # normalizer
             percentile_normalizer = PercentileNormalizer(
-                lower_percentile=0.5,
-                upper_percentile=99.5,
+                lower_percentile=0.1,
+                upper_percentile=99.9,
                 lower_limit=0,
                 upper_limit=1,
             )
@@ -63,18 +63,18 @@ def preprocess(inputDir):
                     modality_name="t1",
                     input_path=t1File,
                     output_path=prep_dir + "/" + inputDir.name + "_t1.nii.gz",
-                    bet=False,
+                    bet=True,
                     normalizer=percentile_normalizer,
                 ),
                 Modality(
                     modality_name="t2",
                     input_path=t2File,
                     output_path=prep_dir + "/" + inputDir.name + "_t2.nii.gz",
-                    bet=False,
+                    bet=True,
                     normalizer=percentile_normalizer,
                 ),
                 Modality(
-                    modality_name="fla",
+                    modality_name="flair",
                     input_path=flaFile,
                     output_path=prep_dir + "/" + inputDir.name + "_fla.nii.gz",
                     bet=True,