|
@@ -59,7 +59,12 @@ def process_files(input_path, output_path, create_figures, save_nifti_mask):
|
|
|
# Create the temp path to search for dwi_masks
|
|
|
temp_path = os.path.join(os.path.dirname(file_path), "RegisteredTractMasks_adjusted")
|
|
|
dwi_masks = glob.glob(os.path.join(temp_path, "*dwi_flipped.nii.gz"))
|
|
|
-
|
|
|
+ white_matter_index = next((i for i, path in enumerate(dwi_masks) if "White_matter" in path), None)
|
|
|
+ white_matter_path = dwi_masks.pop(white_matter_index)
|
|
|
+ # Load white matter mask
|
|
|
+ white_matter_img = nib.load(white_matter_path)
|
|
|
+ white_matter_data = white_matter_img.get_fdata()
|
|
|
+
|
|
|
# Load DWI data using nibabel
|
|
|
dwi_img = nib.load(file_path)
|
|
|
dwi_data = dwi_img.get_fdata()
|
|
@@ -83,10 +88,11 @@ def process_files(input_path, output_path, create_figures, save_nifti_mask):
|
|
|
# Assuming you want to calculate the average value within the mask region
|
|
|
for pp in pix_dialation:
|
|
|
if pp != 0:
|
|
|
- mask_data = binary_dilation(mask_data_pre_dilation, iterations=pp)
|
|
|
+ mask_data0 = binary_dilation(mask_data_pre_dilation, iterations=pp)
|
|
|
else:
|
|
|
- mask_data = mask_data_pre_dilation > 0
|
|
|
+ mask_data0 = mask_data_pre_dilation > 0
|
|
|
|
|
|
+ mask_data = mask_data0 & (white_matter_data > 0)
|
|
|
if stroke_path:
|
|
|
stroke_image = nib.load(stroke_path)
|
|
|
stroke_data = stroke_image.get_fdata()
|