#!/bin/bash

定义输入和输出目录

input_dir="your_input_directory" output_dir="your_output_directory"

创建输出目录

mkdir -p $output_dir

遍历输入目录中的.nii文件

for file in $input_dir/*.nii; do

提取文件名

filename=$(basename "$file" .nii)

异源图像配标

flirt -in $file -ref MNI152_T1_2mm.nii.gz -out ${output_dir}/${filename}_aligned.nii.gz -omat ${output_dir}/${filename}_aligned.mat -bins 256 -cost corratio -searchrx -180 180 -searchry -180 180 -searchrz -180 180 -dof 12 -interp trilinear

图像分割

bet ${output_dir}/${filename}_aligned.nii.gz ${output_dir}/${filename}_brain.nii.gz -f 0.5 -g 0 -m

去除小脑

fslmaths ${output_dir}/${filename}_brain.nii.gz -mul ${output_dir}/${filename}_brain_mask.nii.gz ${output_dir}/${filename}_brain_no_cerebellum.nii.gz

标准化

fslmaths ${output_dir}/${filename}_brain_no_cerebellum.nii.gz -inm 10000 ${output_dir}/${filename}_brain_no_cerebellum_normalized.nii.gz done

echo "Batch processing completed.