8-1-数据预处理工具

2023-08-05

字数统计: 466字 | 阅读时长: 2分

× 文章目录

1. 创建每个步骤对应的文件夹
2. 提取配准后的文件到7.Co-register文件夹

Author: haoransun
Wechat: SHR—97

Matlab
SPM12 https://www.fil.ion.ucl.ac.uk/spm/software/download/
Dpabi http://rfmri.org/dpabi
BrainNetViewer https://www.nitrc.org/projects/bnv/
gretna https://www.nitrc.org/projects/gretna/
AAL https://www.gin.cnrs.fr/en/tools/aal/ https://www.oxcns.org/aal3.html https://search.kg.ebrains.eu/instances/Dataset/f8758eda-483e-45fe-8a88-a1fc806dde18

https://blog.csdn.net/txapples/article/details/108471097

创建每个步骤对应的文件夹

Text

## 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.Co-register
# * 8.ROI


import os
import shutil
import glob

# 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/*/*"))

提取配准后的文件到7.Co-register文件夹

Text

## 提取配准后的文件到7.Co-register文件夹
# * 140个文件/人
# * rswras

base_dir = "/home/pugongying/data/Brain/fMRI-Test/ADNI/*"
base_folders = (glob.glob(base_dir))
for base_folder in base_folders:
    co_register_tmp_list = glob.glob(os.path.join(base_folder, "Resting_State_fMRI/*/2.NiFTI/rswras*.nii"))
    dst_folders = glob.glob(os.path.join(base_folder, "Resting_State_fMRI/*/7.Co-register/"))[0]
    for co_register_tmp in co_register_tmp_list:
        shutil.copy(co_register_tmp, dst_folders)

Dpabi提取ROI信号