DTI数据分析fsl软件常用指令

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已于 2024-05-12 22:54:11 修改

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于 2024-01-21 11:34:51 首次发布

本文链接：https://blog.csdn.net/weixin_43267559/article/details/135727284

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这篇文章详细描述了使用FSL(FMRIBSoftwareLibrary)进行扩散张量成像(DTI)数据预处理、统计分析和纤维束追踪的过程，包括TBSS(Tract-BasedSpatialStatistics)和TFCE(Threshold-FreeClusterEnhancement)方法，以及相关可视化步骤。

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fslmaths tbss_tfce_corrp_tstat1 -thr 0.95 grot

tbss_deproject grot 1

tbss_deproject grot 2

fslview all_FA grot_to_all_FA -l Red-Yellow

fslview ../FA/subject_001_FA subject_001_FA_grot -l Red-Yellow

fdr -i tbss_tstat1 --oneminusp -m mean_FA_skeleton_mask -q 0.05 --othresh=thresh_tbss_tstat1 && autoaq -i thresh_tbss_tstat1 -a "JHU ICBM-DTI-81 White-Matter Labels" -o autoaq_JHU81_thresh_tbss_tstat_1.txt -t 0.95

fdr -i tbss_tstat2 --oneminusp -m mean_FA_skeleton_mask -q 0.05 --othresh=thresh_tbss_tstat2 && autoaq -i thresh_tbss_tstat2 -a "JHU ICBM-DTI-81 White-Matter Labels" -o autoaq_JHU81_thresh_tbss_tstat_2.txt -t 0.95

fslhd *.nii.gz

/home/xiangya/mricron_lx/dcm2nii -4 y MR****

fslroi ${heading}00${a}.nii.gz b0 0 1

bet2 b0.nii.gz nodif_brain -m -f 0.2

eddy_correct ${heading}00${a}.nii.gz data 0

dtifit --data=data.nii.gz --out=${heading}00${a} --mask=nodif_brain_mask --bvecs=${heading}00${a}.bvec --bvals=${heading}00${a}.bval

tbss_1_preproc *.nii.gz

tbss_2_reg -T

tbss_3_postreg -S

tbss_4_prestats 0.2

tbss_non_FA AD && tbss_non_FA RD && tbss_non_FA MD

design_ttest2 design n n

randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -e design.grp -n 5000 --T2 --uncorrp

randomise -i all_FA_skeletonised -o PairedT -d design.mat -t design.con -e design.grp -m mean_FA_skeleton_mask -n 5000 --T2 --uncorrp

randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design.mat -t design.con -f design.fts -e design.grp -n 5000 --T2 --uncorrp

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

tbss_fill tbss_tfce_corrp_tstat1 0.95 mean_FA tbss_fill

cluster -i tbss_tfce_corrp_tstat1.nii.gz -t 0.95 -o clusters

fslmaths clusters.nii.gz -thr 1 -uthr 1 -bin cluster1

fslmaths cluster1.nii.gz -bin cluster1_mask

fslmaths clusters.nii.gz -thr 0.95 -bin clusters_mask

fslmeants -i all_FA_skeletonised -m clusters_mask.nii.gz -o clusters_mask.txt

for num in 63 64 65 66 67;

do fslmaths tfce_0.99_clusters1.nii.gz -thr ${num} -uthr ${num} -bin tfce_0.99_clusters1_${num}_mask;

done

for num in 63 64 65 66 67;

do fslmeants -i all_FA_skeletonised -m tfce_0.99_clusters1_${num}_mask.nii.gz -o tfce_0.99_clusters1_${num}.txt;

done

autoaq -i tbss_tfce_corrp_tstat1 -a "JHU ICBM-DTI-81 White-Matter Labels" -o autoaq_JHU81_corrp_1.txt -t 0.95

autoaq -i tbss_tfce_corrp_tstat1 -a "JHU White-Matter Tractography Labels" -o autoaq_JHU81_corrp_1.txt -t 0.95

fslmaths tbss_tfce_corrp_fstat1.nii.gz -thr 0.95 -bin ftest_mask

fslmaths tbss_tfce_corrp_tstat1.nii.gz -thr 0.95 -bin corrp_1_mask

fslmaths mean_FA_skeleton_mask -mul corrp_1_mask mask

tbss_1_preproc *.nii.gz && tbss_2_reg -T && tbss_3_postreg -S && tbss_4_prestats 0.2 && tbss_non_FA AD && tbss_non_FA RD && tbss_non_FA MD

for num in 001 002 003 004 005 006 007 008 009 010 011 012 013 014 015 016 017 018 019 020 021 022 023 024 025 026 027 028 029 030 031 032 033 034 035 036 037 038 039 040 041 042 043 044 045 046 047 048 049 050 051 052 053 054 055 056 057 058 059 060 061 062 063 064 065 066 067 068 069 070 071 072 073 074 075 076 077 078 079 080 081 082 083 084 085 086 087 088 089 090 091 092 093 094 095 096 097 098 099 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219;

do bedpostx_gpu sub${num};

for num in 001 004 005 014 062 064;

do probtrackx2_gpu -x /home/msi/followup/grot/sbb${num}_FA_FA_grot.nii.gz -l --onewaycondition -c 0.2 -S 2000 --steplength=0.5 -P 5000 --fibthresh=0.01 --distthresh=0.0 --sampvox=0.0 --forcedir --opd -s /home/msi/followup/cs2/P${num}.bedpostX/merged -m /home/msi/followup/cs2/P${num}.bedpostX/nodif_brain_mask --dir=/home/msi/followup/outcome/sbb${num};

done

for num in 1 2 3 4 5 6 7 8 9 10;

do autoaq -i tbss_tfce_corrp_tstat${num} -a "JHU ICBM-DTI-81 White-Matter Labels" -o tbss_tfce_corrp_tstat${num}.txt -t 0.95;

done