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- # -*- coding: utf-8 -*-
- import os
- import nibabel as nib
- import numpy as np
- # Set up the directory paths
- code_dir = os.path.dirname(os.path.abspath(__file__))
- parent_dir = os.path.dirname(code_dir)
- file_path = os.path.join(parent_dir, "input", "C57BL6_mouse_qa.nii.gz")
- output_path = os.path.join(parent_dir, "output", "C57BL6_mouse_qa.nii.gz")
- # Load the image
- img = nib.load(file_path)
- data = img.get_fdata()
- # Thresholding
- threshold_value = 0.3 * np.max(data)
- mask_data = np.where(data >= threshold_value, 1, 0)
- # Save the mask
- output_path = output_path.replace("C57BL6_mouse_qa.nii.gz", "White_matter_mask.nii.gz")
- mask_img = nib.Nifti1Image(mask_data, img.affine)
- nib.save(mask_img, output_path)
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