AFNI 常用命令实例

最新推荐文章于 2024-01-21 11:34:51 发布

TODAIZHANG

最新推荐文章于 2024-01-21 11:34:51 发布

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分类专栏： LINUX文件处理常用代码医学图像处理

本文链接：https://blog.csdn.net/TODAIZHANG/article/details/112398036

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AFNI 常用命令实例

1. dtifit计算FA值

#! /bin/csh

set DATA_dir=/nfs/m1/hcp
set target_dir=/nfs/s2/userhome/zhouke/SubcortexSegmentation

foreach sub_id (`awk '{print}' /nfs/s2/userhome/zhouke/SubcortexSegmentation/subjectList.txt`)
	cd ${target_dir}
	
    echo ${sub_id}
	mkdir ${sub_id}
	cd ${sub_id}

	# calculating FA value 
	dtifit -k ${DATA_dir}/${sub_id}/T1w/Diffusion_7T/data.nii.gz -o dti -r ${DATA_dir}/${sub_id}/T1w/Diffusion_7T/bvecs -b ${DATA_dir}/${sub_id}/T1w/Diffusion_7T/bvals -m ${DATA_dir}/${sub_id}/T1w/Diffusion_7T/nodif_brain_mask.nii.gz
	cd ..
end

2. 3dresample reslice图像

#! /bin/csh

set DATA_dir=/nfs/m1/hcp
set target_dir=/nfs/s2/userhome/zhouke/SubcortexSegmentation

foreach sub_id (`awk '{print}' /nfs/s2/userhome/zhouke/SubcortexSegmentation/subjectList.txt`)
	cd ${target_dir}/${sub_id}

	# resample from 0.7mm to 1.05mm 
	cp -r ${DATA_dir}/${sub_id}/T1w/T1w_acpc_dc_restore_brain.nii.gz ${target_dir}/${sub_id}
	3dresample -dxyz 1.05 1.05 1.05 -prefix T1w_acpc_dc_restore_brain_105.nii.gz -input T1w_acpc_dc_restore_brain.nii.gz
	
	cp -r ${DATA_dir}/${sub_id}/T1w/T2w_acpc_dc_restore_brain.nii.gz ${target_dir}/${sub_id}
	3dresample -dxyz 1.05 1.05 1.05 -prefix T2w_acpc_dc_restore_brain_105.nii.gz -input T2w_acpc_dc_restore_brain.nii.gz
end

3. 3dTcat对多个数据进行time series串联

#! /bin/csh

set DATA_dir=/nfs/m1/hcp
set target_dir=/nfs/s2/userhome/zhouke/SubcortexSegmentation

foreach sub_id (`awk '{print}' /nfs/s2/userhome/zhouke/SubcortexSegmentation/subjectList.txt`)
	cd ${target_dir}/${sub_id}
	
	# 3dTcat in time series
	3dTcat -relabel -prefix ${sub_id}_T1w_T2w_FA.nii.gz T1w_acpc_dc_restore_brain_105.nii.gz T2w_acpc_dc_restore_brain_105.nii.gz dti_FA.nii.gz
end