9-(图)利用Matlab的spm12工具处理fMRI为ROI

2023-10-28

字数统计: 1.2k字 | 阅读时长: 5分

× 文章目录

1. 1. 下载DICOM格式数据
2. 2. DICOM -> NIFTI格式输出s开头文件
3. 3. 时间层校正Slice Timing 输出as开头文件
4. 4. 头动校正Realignment 输出ras开头文件
5. 5. 归一化Normalize 输出w开头文件
6. 6. 平滑Smooth 输出sw开头文件
7. 7. 配准Co-register reslice
8. 8. 提取ROI

Author: haoransun
Wechat: SHR—97

下载DICOM格式数据
DICOM -> NIFTI格式输出s开头文件
时间层校正Slice Timing 输出as开头文件
头动校正Realignment 输出ras开头文件
归一化Normalize 输出w开头文件
平滑Smooth 输出sw开头文件
配准Co-register reslice
提取ROI
1. 下载DICOM格式数据
登录地址：

https://ida.loni.usc.edu/ladvq_search.xjsp?project=ADNI&page=SEARCH&subPage=ADV_QUERY

输入登录账号及密码->ADNI GO->DOWNLOAD IMAGE Collections->Advanced Search(beta)->

确定Research Group: EMCI LCMI AD CN

Image Description:Resting State fMRI-> Display in result->csv download （注：网页加载很慢）

建议单个下，如果all同时下，会出现断网，网中断，下载失败或文件不全。且不好统计哪些是下载过的**。**

已知下载好的文件格式解压如下（注：文件必须是6720个dicom，如果少了，说明网络中断导致文件没下载全，需要重新下载。）：

事先在每个subject里存好每个步骤对应路径（可以用程序在每个人对应路径下创建以下文件夹）:

import os
import shutil
import glob

## 在每个subject下面提前创建每个步骤对应的文件夹
# * 2.NiFTI
# * 3.SliceTime
# * 4.Realignment
# * 5.Normalize
# * 6.Smooth
# * 7.ROI

# 原始的dcm文件每个subject有6720个dicom,少了，则是网络中断，需要重新下载
prefix_dir = "/home/pugongying/data/Brain/fMRI-Test/ADNI/"
nifti_folder_name = "2.NiFTI"
sliceTime_folder_name = "3.SliceTime"
realignment_folder_name = "4.Realignment"
normalize_folder_name = "5.Normalize"
smooth_folder_name = "6.Smooth"
co_register_folder_name = "7.Co-register"
ROI_folder_name = "8.ROI"

folders = glob.glob(os.path.join(prefix_dir, "*/Resting_State_fMRI/*"))


for folder in folders:
    if not os.path.exists(os.path.join(folder, nifti_folder_name)):
        os.makedirs(os.path.join(folder, nifti_folder_name))

    if not os.path.exists(os.path.join(folder, sliceTime_folder_name)):
        os.makedirs(os.path.join(folder, sliceTime_folder_name))

    if not os.path.exists(os.path.join(folder, realignment_folder_name)):
        os.makedirs(os.path.join(folder, realignment_folder_name))

    if not os.path.exists(os.path.join(folder, normalize_folder_name)):
        os.makedirs(os.path.join(folder, normalize_folder_name))

    if not os.path.exists(os.path.join(folder, smooth_folder_name)):
        os.makedirs(os.path.join(folder, smooth_folder_name))

    if not os.path.exists(os.path.join(folder, co_register_folder_name)):
        os.makedirs(os.path.join(folder, co_register_folder_name))

    if not os.path.exists(os.path.join(folder, ROI_folder_name)):
        os.makedirs(os.path.join(folder, ROI_folder_name))


glob.glob(os.path.join(prefix_dir, "*/Resting_State_fMRI/*/*"))