tbss链接地址

#! /bin/bash/

#1) move control and time1 group data into one dirtory

#ziyuan mulu
data_path="/home/mcbrain/sharefolder/data"

#con data  dir
con_data="/home/mcbrain/sharefolder/data/control/dti_1to210nii_final"
#time1 data dir
time1_data="/home/mcbrain/sharefolder/data/time1/dti_time1_nii"

#make new dir contain con and time1
mkdir ${data_path}/con_time1_dti

#move con and time data to con_time1_dti
#con
cp -r ${con_data}/subc* ${data_path}/con_time1_dti/
cp -r ${time1_data}/subt* ${data_path}/con_time1_dti/

##2)  tbss

input="${data_path}/con_time1_dti"
ls $input |while read line;do
echo ${line}
fslroi ${input}/${line}/Dwi/${line}.nii.gz ${input}/${line}/Dwi/${line}_b0 0 1
bet ${input}/${line}/Dwi/${line}_b0.nii.gz ${input}/${line}/Dwi/${line}_nodif_brain -m -f 0.2
eddy_correct ${input}/${line}/Dwi/${line}.nii ${input}/${line}/Dwi/${line}_data.nii 0
dtifit --data=${input}/${line}/Dwi/${line}_data.nii.gz --out=${input}/${line}/Dwi/${line}_data --mask=${input}/${line}/Dwi/${line}_nodif_brain_mask.nii.gz --bvecs=${input}/${line}/Dwi/${line}.bvec --bvals=${input}/${line}/Dwi/${line}.bval
fslmaths ${input}/${line}/Dwi/${line}_data_L2.nii.gz -add ${input}/${line}/Dwi/${line}_data_L3.nii.gz -div 2 ${input}/${line}/Dwi/${line}_RD.nii.gz
done

##3)move FA.nii into one directory
mkdir ${data_path}/tbss
input="${data_path}/con_time1_dti"
ls $input |while read line;do
cp -r ${input}/${line}/Dwi/${line}_data_FA.nii.gz ${data_path}/tbss
done

cd ${data_path}/tbss
tbss_1_preproc *.nii.gz
tbss_2_reg -T
tbss_3_postreg -S
tbss_4_prestats 0.2

#切换到stat目录下
cd ../stats
#两组用design_ttest2，三组用fsl中的GlmGUI来设计，7和11分别表示组1正常，组2患者组
design_ttest2 design 7 11

#randomise分析命令：
randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask-d design.mat -t design.con -n 5000 --T2
#观察结果：
fslview $FSLDIR/data/standard/MNI152_T1_1mm mean_FA_skeleton -l Green -b 0.2,0.8 tbss_tstat1 -l Red-Yellow -b 3,6 tbss_tstat2 -l Blue-Lightblue -b 3,6
fslview $FSLDIR/data/standard/MNI152_T1_1mm mean_FA_skeleton -l Green -b 0.2,0.7 tbss_tfce_corrp_tstat1 -l Red-Yellow -b 0.95,1

#对结果进行填充及显示：
tbss_fill tbss_tfce_corrp_tstat1 0.95 mean_FA tbss_fill1
fslview mean_FA -b 0,0.6 mean_FA_skeleton -l Green -b 0.2,0.7 tbss_fill1 -l Red-Yellow