Merge 8c42a39 into c8b5d66

AthenaEPI · May 11, 2020 · ba79a93 · ba79a93
2 parents c8b5d66 + 8c42a39
commit ba79a93
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Showing 2 changed files with 12 additions and 3 deletions.
diff --git a/dmipy/tissue_response/three_tissue_response.py b/dmipy/tissue_response/three_tissue_response.py
@@ -82,7 +82,10 @@ def three_tissue_response_dhollander16(
     SDM = signal_decay_metric(acquisition_scheme, data)
 
     # Make Mask
-    b0_mask, mask = median_otsu(data, median_radius=2, numpass=1)
+    b0_mask, mask = median_otsu(
+        input_volume=data,
+        vol_idx=np.where(acquisition_scheme.b0_mask)[0],
+        median_radius=4, numpass=4)  # based on dipy default
     gtab = gtab_dmipy2dipy(acquisition_scheme)
     tenmod = dti.TensorModel(gtab)
     tenfit = tenmod.fit(b0_mask)

diff --git a/dmipy/tissue_response/white_matter_response.py b/dmipy/tissue_response/white_matter_response.py
@@ -51,7 +51,10 @@ def white_matter_response_tournier07(
 
     if data.ndim == 4:
         # calculate brain mask on 4D data (x, y, z, DWI)
-        b0_mask, mask = median_otsu(data, 2, 1)
+        b0_mask, mask = median_otsu(
+            input_volume=data,
+            vol_idx=np.where(acquisition_scheme.b0_mask)[0],
+            median_radius=4, numpass=4)  # based on dipy default
         # needs to be eroded 3 times.
         mask_eroded = binary_erosion(mask, iterations=3)
         data_to_fit = data[mask_eroded]
@@ -153,7 +156,10 @@ def white_matter_response_tournier13(
 
     if data.ndim == 4:
         # calculate brain mask on 4D data (x, y, z, DWI)
-        b0_mask, mask = median_otsu(data, 2, 1)
+        b0_mask, mask = median_otsu(
+            input_volume=data,
+            vol_idx=np.where(acquisition_scheme.b0_mask)[0],
+            median_radius=4, numpass=4)  # based on dipy default
         # needs to be eroded 3 times.
         mask_eroded = binary_erosion(mask, iterations=3)
         data_to_fit = data[mask_eroded]