ANTs对颅脑结构项MRI预处理流程

琵琶枇杷

已于 2023-08-05 22:25:41 修改

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文章标签：开源 mr bash

于 2023-08-04 16:53:19 首次发布

本文链接：https://blog.csdn.net/cxsunn/article/details/132106244

版权

首先根据ANTs官方文档下载ANTs，mac or linux下载教程，win10以上系统则需要先安装wsl，然后再根据官方文档下载ANTs

在配置过程中遇到任何问题一般都可以从现有博客中找到解决方案，如果在git clone的时候一直连接不上，可以选择把ANTs整个下载下来，放到对应目录下就行

现在主要讲如何用ANTs对颅脑MRI进行预处理，处理顺序依次为：N4偏置场校正—配准—去颅骨

N4偏置场校正：

ANTs提供了官方示例，具体每个参数是什么含义可以去官方文档查询，无脑使用的话就把对应图像路径换掉就行

N4BiasFieldCorrection -d 3 -i /path/to/input_image.nii.gz -o /path/to/output_corrected.nii.gz

实际应用过程中手动依次对单个序列图像处理不现实，写了个对应脚本

#!/bin/bash

# set -x
function read_dir_file(){
	for FILE in $(ls $1)
	do
		if [ -d "${1}/${FILE}" ]
		then
			sub_dir="${1}/${FILE}"
			read_dir_file $sub_dir
			
		else
			# echo "${1}/${FILE}"
			local goal_t1="t1.nii"
			local goal_t2="t2.nii"
			local goal_ce="ce.nii"
			local name=$FILE
			# echo $FILE
			if [ $name = $goal_t1 ]
			then
				t1="${1}/${name}"
				echo "${t1} is being N4BiasFieldCorrected...."
				N4BiasFieldCorrection -d 3 -i ${t1} -o ${1}/N4_t1.nii
			elif [ $name = $goal_t2 ]
			then
				t2="${1}/${name}"
				echo "${t2} is being N4BiasFieldCorrected...."
				N4BiasFieldCorrection -d 3 -i ${t2} -o ${1}/N4_t2.nii
			elif [ $name = $goal_ce ]
			then
				ce="${1}/${name}"
				echo "${ce} is being N4BiasFieldCorrected...."
				N4BiasFieldCorrection -d 3 -i ${ce} -o ${1}/N4_ce.nii
			fi
		fi
	done
}

read_dir_file /mnt/e/path/to/mri
# set +x

图像配准：

如果其中某个序列勾画了ROI，则把其他序列配准到有ROI的序列

antsRegistrationSyNQuick.sh -d 3 -f target.nii -m ori.nii -o $prefix

$prefix 是你生成新文件的前缀，运行此命令后会生成两个重要的nii文件

prefix_warped.nii 是 ori.nii 朝 target.nii配准后的新文件，prefix_inversewarped.nii 是 target.nii 朝 ori.nii配准的新文件

批处理脚本

#!/bin/bash

# set -x
function read_dir_file(){
	for FILE in $(ls $1)
	do
		if [ -d "${1}/${FILE}" ]
		then
			sub_dir="${1}/${FILE}"
			read_dir_file $sub_dir
			
		else
			# echo "${1}/${FILE}"
			local goal_t1="N4_t1.nii"
			local goal_ce="N4_ce.nii"
			local name=$FILE
			local t2="${1}/N4_t2.nii"
			# echo $FILE
			if [ $name = $goal_t1 ]
			then
				t1="${1}/${name}"
				# echo "${1}/${name} is being registered..."
				bash /opt/ANTs/bin/antsRegistrationSyNQuick.sh -d 3 -f ${t2} -m ${t1} -o ${1}/t1_to_t2_
			elif [ $name = $goal_ce ]
			then
				ce="${1}/${name}"
				# echo "${1}/${name} is being registered..."
				bash /opt/ANTs/bin/antsRegistrationSyNQuick.sh -d 3 -f ${t2} -m ${ce} -o ${1}/ce_to_t2_
			fi
		fi
	done
}

read_dir_file /mnt/e/path/to/mri
# set +x

去颅骨：

先下载一个没有颅骨的模板数据，可以下载ANTs中的OASIS，里边是T1的相关数据

antsBrainExtraction.sh -d 3 -a ori.nii -e T_template0.nii.gz -m T_template0_BrainCerebellumProbabilityMask.nii.gz -o $prefix

批处理脚本

#!/bin/bash

# set -x
function read_dir_file(){
	for FILE in $(ls $1)
	do
		if [ -d "${1}/${FILE}" ]
		then
			sub_dir="${1}/${FILE}"
			read_dir_file $sub_dir
			
		else
			# echo "${1}/${FILE}"
			local goal_t1="t1_to_t2_Warped.nii.gz"
			local goal_ce="ce_to_t2_Warped.nii.gz"
			local goal_t2="N4_t2.nii"
			local name=$FILE
			local templete="/mnt/e/path/to/AOSIS/T_template0.nii.gz"
			local mask="/mnt/e/path/to/AOSIS/T_template0_BrainCerebellumProbabilityMask.nii.gz"
			# echo $FILE
			if [ $name = $goal_t1 ]
			then
				t1="${1}/${name}"
				# echo "${t1} is being BrainExtracted...."
				bash /opt/ANTs/bin/antsBrainExtraction.sh -d 3 -a ${t1} -e ${templete} -m ${mask} -o ${1}/t1_
			elif [ $name = $goal_t2 ]
			then
				t2="${1}/${name}"
				# echo "${t2} is being BrainExtracted...."
				bash /opt/ANTs/bin/antsBrainExtraction.sh -d 3 -a ${t2} -e ${templete} -m ${mask} -o ${1}/t2_
			elif [ $name = $goal_ce ]
			then
				ce="${1}/${name}"
				# echo "${ce} is being BrainExtracted...."
				bash /opt/ANTs/bin/antsBrainExtraction.sh -d 3 -a ${ce} -e ${templete} -m ${mask} -o ${1}/ce_
			fi
		fi
	done
}

read_dir_file /mnt/e/path/to/mri
# set +x