影像组学视频学习笔记(22)-从atlas抠出想要的ROI做成mask文件、Li‘s have a solution and plan.

本笔记来源于B站Up主: 有Li 的影像组学系列教学视频
本节(22)主要讲解: 从atlas抠出想要的ROI做成mask

0. Task: 将某个特定的脑功能区(这里以10为例)设置为mask

1. 导入包

# pip install nibabel    ## for the first time
import numpy as np
import nibabel as nib
import os
from collections import Counter

2. 读入文件

roiIndex = 10
basePath = 'C:/Users/RONG/Desktop/roi2mask/'
atlasName = "aal.nii.gz"
atlasFile = os.path.join(basePath, atlasName)

atlas_nii = nib.load(atlasFile)
atlas_arr = atlas_nii.get_fdata()

3. 设置

mask_arr = atlas_arr.copy()
mask_arr[atlas_arr != roiIndex] = 0
mask_arr[atlas_arr == roiIndex] = 1
mask_affine = atlas_nii.affine.copy()
mask_hrd = atlas_nii.header.copy()
mask_hrd["cal_max"] = 1
######## print(mask_hrd)

mask_nii = nib.Nifti1Image(mask_arr, mask_affine, mask_hrd)
nib.save(mask_nii,os.path.join(basePath, “roi_” + str(roiIndex) + “.nii.gz”))
#print(Counter(mask_arr.flatten()))

4. 查看结果(如图)

作者：北欧森林
链接：https://www.jianshu.com/p/e0f11189c642
来源：简书，已获授权转载

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