ANTS处理nii数据

去除非脑组织，使用Oasis模板

#!/bin/bash
#ls>sublist.txt #此命令用于创建文件列表
#增加.sh的可执行权限，chmod +x *.sh
sour_dir=/mnt/E:/CNN
T0=/mnt/E:/CNN/template/T_template0.nii.gz
T_prob=/mnt/E:/CNN/template/T_template0_BrainCerebellumProbabilityMask.nii.gz
T_reg=/mnt/E:/CNN/template/T_template0_BrainCerebellumRegistrationMask.nii.gz
hc=${sour_dir}/nj_hc/nj_hc.txt
sp=${sour_dir}/nj_sp/nj_sp.txt
sh_hc=${sour_dir}/sh_hc/sh_hc.txt
sh_sp=${sour_dir}/sh_sp/sh_sp.txt
for sub in  `cat  ${sp}`
do
        echo ${sub}
        cd ${sour_dir}/nj_sp
#	mkdir ${sour_dir}/${sub%%.*.*}
        antsBrainExtraction.sh -d 3 -a ${sub} -e ${T0} \
		-m ${T_prob} \
		-f ${T_reg}  \
		-o ${sour_dir}/nj_sp_processed/${sub%%.*} 
done

for sub in  `cat  ${sh_hc}`
do
        echo ${sub}
        cd ${sour_dir}/sh_hc
#	mkdir ${sour_dir}/${sub%%.*.*}
        antsBrainExtraction.sh -d 3 -a ${sub} -e ${T0} \
		-m ${T_prob} \
		-f ${T_reg}  \
		-o ${sour_dir}/sh_hc_processed/${sub%%.*} 
done
for sub in  `cat  ${sh_sp}`
do
        echo ${sub}
        cd ${sour_dir}/sh_sp
#	mkdir ${sour_dir}/${sub%%.*.*}
        antsBrainExtraction.sh -d 3 -a ${sub} -e ${T0} \
		-m ${T_prob} \
		-f ${T_reg}  \
		-o ${sour_dir}/sh_sp_processed/${sub%%.*} 
done