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