{"id":41074,"date":"2025-05-31T06:02:12","date_gmt":"2025-05-30T22:02:12","guid":{"rendered":"https:\/\/www.wsisp.com\/helps\/41074.html"},"modified":"2025-05-31T06:02:12","modified_gmt":"2025-05-30T22:02:12","slug":"ubuntu-%e5%ae%89%e8%a3%85-fsl-%e5%8f%8a%e5%a4%9a%e6%a8%a1%e6%80%81%e8%84%91mri%e7%9a%84%e5%8e%bb%e9%a2%85%e9%aa%a8%e5%a4%84%e7%90%86%ef%bc%88%e5%90%ab-hd-bet-%e6%b7%b1%e5%ba%a6%e5%ad%a6%e4%b9%a0","status":"publish","type":"post","link":"https:\/\/www.wsisp.com\/helps\/41074.html","title":{"rendered":"Ubuntu \u5b89\u88c5 FSL \u53ca\u591a\u6a21\u6001\u8111MRI\u7684\u53bb\u9885\u9aa8\u5904\u7406\uff08\u542b HD-BET \u6df1\u5ea6\u5b66\u4e60\u65b9\u6cd5\uff09"},"content":{"rendered":"

\u8111\u90e8\u533b\u5b66\u56fe\u50cf\u5904\u7406\u7684\u7b2c\u4e00\u6b65\u901a\u5e38\u662f\u53bb\u9885\u9aa8（Skull Stripping），\u4e5f\u53eb\u8111\u63d0\u53d6（Brain Extraction）\u3002\u672c\u6587\u5c06\u4ecb\u7ecd\u5982\u4f55\u5728 Ubuntu \u7cfb\u7edf\u4e2d\u5b89\u88c5 FSL，\u4f7f\u7528\u5176\u7ecf\u5178\u5de5\u5177 BET \u8fdb\u884c T1\u3001T2\u3001PD \u6a21\u6001\u7684\u53bb\u9885\u9aa8\u64cd\u4f5c，\u5e76\u8865\u5145\u4ecb\u7ecd\u57fa\u4e8e\u6df1\u5ea6\u5b66\u4e60\u7684\u66f4\u5f3a\u5927\u65b9\u6cd5 HD-BET\u3002<\/p>\n

\n

📦 \u4e00\u3001FSL \u5b89\u88c5\u4e0e\u73af\u5883\u914d\u7f6e（Ubuntu）<\/h3>\n

FSL（FMRIB Software Library）\u662f\u725b\u6d25\u5927\u5b66\u5f00\u53d1\u7684\u533b\u5b66\u56fe\u50cf\u5904\u7406\u5de5\u5177\u96c6，\u652f\u6301\u5927\u591a\u6570\u795e\u7ecf\u5f71\u50cf\u64cd\u4f5c\u3002<\/p>\n

1. \u5b89\u88c5\u4f9d\u8d56（\u63a8\u8350）<\/h4>\n

sudo apt update
\nsudo apt install -y curl wget bzip2 <\/p>\n

2. \u4e0b\u8f7d\u5e76\u8fd0\u884c\u5b89\u88c5\u5668<\/h4>\n

curl -sSL https:\/\/fsl.fmrib.ox.ac.uk\/fsldownloads\/fslinstaller.py -o fslinstaller.py
\npython3 fslinstaller.py <\/p>\n

\u5b89\u88c5\u8fc7\u7a0b\u4e2d\u4f1a\u63d0\u793a\u9009\u62e9\u8def\u5f84，\u8fd9\u91cc\u4ee5 \/home\/software\/fsl \u4e3a\u4f8b\u3002<\/p>\n

3. \u914d\u7f6e\u73af\u5883\u53d8\u91cf<\/h4>\n

\u5c06\u4ee5\u4e0b\u5185\u5bb9\u6dfb\u52a0\u5230\u4f60\u7684 ~\/.bashrc \u6587\u4ef6\u4e2d：<\/p>\n

echo "export FSLDIR=\/home\/software\/fsl" >> ~\/.bashrc
\necho ". \\\\$FSLDIR\/etc\/fslconf\/fsl.sh" >> ~\/.bashrc
\necho "export PATH=\\\\$FSLDIR\/bin:\\\\$PATH" >> ~\/.bashrc <\/p>\n

\u7136\u540e\u5237\u65b0\u914d\u7f6e：<\/p>\n

source ~\/.bashrc <\/p>\n

4. \u6d4b\u8bd5\u5b89\u88c5<\/h4>\n

which bet <\/p>\n

\u8f93\u51fa\u5e94\u4e3a \/home\/software\/fsl\/bin\/bet，\u8bf4\u660e\u5b89\u88c5\u6210\u529f\u3002<\/p>\n

<\/h3>\n

\u4e8c\u3001\u4f7f\u7528 FSL \u7684 BET \u5de5\u5177\u8fdb\u884c\u53bb\u9885\u9aa8\u5904\u7406<\/h3>\n

BET（Brain Extraction Tool）\u662f FSL \u4e2d\u7684\u7ecf\u5178\u53bb\u9885\u9aa8\u5de5\u5177\u3002<\/p>\n

1. \u5355\u56fe\u50cf\u5904\u7406\u547d\u4ee4<\/h4>\n

bet input_image.nii.gz output_brain.nii.gz -f 0.5 -g 0 -m <\/p>\n

\u5e38\u7528\u53c2\u6570\u8bf4\u660e：<\/p>\n\n\n\n\n\n\n
\n

\u53c2\u6570<\/p>\n<\/td>\n

\n

\u542b\u4e49<\/p>\n<\/td>\n

\n

\u5efa\u8bae\u503c<\/p>\n<\/td>\n<\/tr>\n

\n

-f<\/p>\n<\/td>\n

\n

\u5f3a\u5ea6\u9608\u503c（fractional intensity）<\/p>\n<\/td>\n

\n

T1: 0.3 ~ 0.5; T2\/PD: 0.4 ~ 0.6<\/p>\n<\/td>\n<\/tr>\n

\n

-g<\/p>\n<\/td>\n

\n

\u5782\u76f4\u504f\u79fb（vertical gradient）<\/p>\n<\/td>\n

\n

-0.1~ 0.2<\/p>\n<\/td>\n<\/tr>\n

\n

-m<\/p>\n<\/td>\n

\n

\u540c\u65f6\u8f93\u51fa\u8111\u7ec4\u7ec7 mask<\/p>\n<\/td>\n

\n

\u5efa\u8bae\u52a0<\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

2. \u5404\u6a21\u6001\u63a8\u8350\u53c2\u6570\u8bbe\u7f6e<\/h4>\n\n\n\n\n\n\n
\n

\u6a21\u6001\u7c7b\u578b<\/p>\n<\/td>\n

\n

\u63a8\u8350 -f<\/p>\n

\u503c<\/p>\n<\/td>\n

\n

\u63a8\u8350 -g<\/p>\n

\u503c<\/p>\n<\/td>\n

\n

\u8bf4\u660e<\/p>\n<\/td>\n<\/tr>\n

\n

T1<\/p>\n<\/td>\n

\n

0.3 ~ 0.5<\/p>\n<\/td>\n

\n

0 ~ 0.1<\/p>\n<\/td>\n

\n

\u5bf9\u6bd4\u5f3a，\u5904\u7406\u6700\u7a33\u5b9a<\/p>\n<\/td>\n<\/tr>\n

\n

T2<\/p>\n<\/td>\n

\n

0.4 ~ 0.6<\/p>\n<\/td>\n

\n

0 ~ 0.2<\/p>\n<\/td>\n

\n

\u7070\u767d\u8d28\u754c\u9650\u6a21\u7cca<\/p>\n<\/td>\n<\/tr>\n

\n

PD<\/p>\n<\/td>\n

\n

0.4 ~ 0.6<\/p>\n<\/td>\n

\n

0 ~ 0.2<\/p>\n<\/td>\n

\n

\u5bf9\u6bd4\u8f83\u5f31，\u5bb9\u6613\u6b8b\u7559\u9885\u9aa8<\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

3. \u6279\u91cf\u5904\u7406\u811a\u672c.sh\u793a\u4f8b<\/h4>\n

#!\/bin\/bash<\/p>\n

input_dir="\/path\/to\/images"
\noutput_dir="\/path\/to\/outputs"<\/p>\n

mkdir -p "$output_dir"<\/p>\n

for file in "$input_dir"\/*.nii.gz; do
\n name=$(basename "$file" .nii.gz)
\n bet "$file" "$output_dir\/${name}_brain.nii.gz" -f 0.5 -g 0.1 -m
\n # bet "$file" "$output_dir\/${name}_brain.nii.gz" -R # \u4f7f\u7528-R\u53c2\u6570\u80fd\u591f\u81ea\u52a8\u8bbe\u7f6e-f\u548c-m\u53c2\u6570
\ndone <\/p>\n

<\/h3>\n

\u26a0\ufe0f \u4e09\u3001\u4e3a\u4ec0\u4e48 BET \u6548\u679c\u4e0d\u591f\u597d？<\/h3>\n

\u867d\u7136 BET \u662f\u65e9\u671f\u4e3b\u6d41\u5de5\u5177，\u4f46\u5b83\u6709\u660e\u663e\u9650\u5236：<\/p>\n

    \n
  • \u539f\u7406\u8001\u65e7，\u57fa\u4e8e\u7403\u5f62\u6a21\u578b，\u65e0\u6cd5\u9002\u5e94\u590d\u6742\u8111\u578b<\/li>\n
  • \u4ec5\u4f9d\u8d56\u56fe\u50cf\u5f3a\u5ea6，\u7f3a\u4e4f\u4e0a\u4e0b\u6587\u7ed3\u6784\u7406\u89e3<\/li>\n
  • \u5bf9 T2\u3001PD\u3001\u80bf\u7624\u7b49\u4e0d\u89c4\u5219\u56fe\u50cf\u8868\u73b0\u5dee<\/li>\n
  • \u65e0\u6cd5\u81ea\u52a8\u9002\u5e94\u4e0d\u540c\u4e2a\u4f53\u5dee\u5f02<\/li>\n<\/ul>\n

    \u56e0\u6b64，\u8fd1\u5e74\u6765\u51fa\u73b0\u4e86\u57fa\u4e8e\u6df1\u5ea6\u5b66\u4e60\u7684\u8111\u63d0\u53d6\u65b9\u6cd5，\u4f8b\u5982 HD-BET\u3002<\/p>\n<\/p>\n

    🤖 \u56db\u3001HD-BET \u5b89\u88c5\u4e0e\u4f7f\u7528（\u6df1\u5ea6\u5b66\u4e60\u7248 BET）<\/h3>\n

    HD-BET \u662f\u5fb7\u56fd\u533b\u5b66\u5f71\u50cf\u4e2d\u5fc3（DKFZ）\u53d1\u5e03\u7684\u5f00\u6e90\u6df1\u5ea6\u5b66\u4e60\u5de5\u5177，\u5177\u6709\u4ee5\u4e0b\u4f18\u70b9：<\/p>\n

      \n
    • \u9002\u7528\u4e8e T1\u3001T2\u3001FLAIR\u3001PD \u7b49\u591a\u6a21\u6001<\/li>\n
    • \u652f\u6301\u8111\u7624\u3001\u513f\u7ae5\u3001\u75c5\u53d8\u7b49\u590d\u6742\u573a\u666f<\/li>\n
    • \u6279\u5904\u7406\u3001\u6613\u7528\u6027\u5f3a，\u51e0\u4e4e\u4e0d\u5931\u8d25<\/li>\n<\/ul>\n

      1. \u5b89\u88c5（Python \u73af\u5883）<\/h4>\n

      pip install hd-bet <\/p>\n

      \u5efa\u8bae\u4f7f\u7528 Python \u22653.7，\u5df2\u5b89\u88c5 PyTorch\u3002<\/p>\n

      2. \u4f7f\u7528\u793a\u4f8b<\/h4>\n

      hd-bet -i \/path\/to\/images -o \/path\/to\/output -device cpu <\/p>\n

      \u53c2\u6570\u8bf4\u660e：<\/p>\n\n\n\n\n\n\n
      \n

      \u53c2\u6570<\/p>\n<\/td>\n

      		\n

      \u542b\u4e49<\/p>\n<\/td>\n<\/tr>\n

      \n

      -i<\/p>\n<\/td>\n

      		\n

      \u8f93\u5165\u6587\u4ef6\u5939（\u6216\u5355\u4e2a\u6587\u4ef6）<\/p>\n<\/td>\n<\/tr>\n

      \n

      -o<\/p>\n<\/td>\n

      		\n

      \u8f93\u51fa\u6587\u4ef6\u5939<\/p>\n<\/td>\n<\/tr>\n

      \n

      -device<\/p>\n<\/td>\n

      		\n

      cpu\u6216 cuda<\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

      3. \u6279\u91cf\u5904\u7406\u652f\u6301<\/h4>\n

      \u53ea\u9700\u5c06\u6240\u6709 NIfTI \u6587\u4ef6（.nii.gz）\u653e\u5165\u4e00\u4e2a\u76ee\u5f55，HD-BET \u4f1a\u81ea\u52a8\u5904\u7406\u3002<\/p>\n

      \n

      \u2705 \u4e94\u3001\u603b\u7ed3\u4e0e\u5efa\u8bae<\/h3>\n\n\n\n\n\n\n\n
      \n

      \u9700\u6c42<\/p>\n<\/td>\n

      		\n

      \u63a8\u8350\u5de5\u5177<\/p>\n<\/td>\n

      		\n

      \u539f\u56e0<\/p>\n<\/td>\n<\/tr>\n

      \n

      \u666e\u901a T1 \u8111\u63d0\u53d6<\/p>\n<\/td>\n

      		\n

      BET（\u52a0 -R -f 0.4）<\/p>\n<\/td>\n

      		\n

      \u5feb\u901f\u3001\u7ecf\u5178<\/p>\n<\/td>\n<\/tr>\n

      \n

      T2\u3001PD\u3001\u75c5\u7076\u56fe\u50cf<\/p>\n<\/td>\n

      		\n

      HD-BET<\/p>\n<\/td>\n

      		\n

      \u9c81\u68d2\u3001\u8de8\u6a21\u6001\u3001\u81ea\u9002\u5e94<\/p>\n<\/td>\n<\/tr>\n

      \n

      \u8111\u7ec4\u7ec7\u5206\u5272（GM\/WM）<\/p>\n<\/td>\n

      		\n

      FSL FAST \/ Freesurfer<\/p>\n<\/td>\n

      		\n

      \u66f4\u7cbe\u7ec6\u7684\u7ed3\u6784\u5206\u5272<\/p>\n<\/td>\n<\/tr>\n

      \n

      \u6279\u91cf\u5904\u7406<\/p>\n<\/td>\n

      		\n

      HD-BET \/ \u81ea\u5199\u811a\u672c<\/p>\n<\/td>\n

      		\n

      \u81ea\u52a8\u5316\u66f4\u9ad8<\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

      📚 \u53c2\u8003\u8d44\u6e90<\/h3>\n
        \n
      • FSL \u5b98\u7f51：https:\/\/fsl.fmrib.ox.ac.uk\/fsl\/fslwiki<\/li>\n
      • HD-BET Github：https:\/\/github.com\/MIC-DKFZ\/HD-BET<\/li>\n
      • BET \u4f7f\u7528\u624b\u518c：bet -h<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"

        \u6587\u7ae0\u6d4f\u89c8\u9605\u8bfb490\u6b21\uff0c\u70b9\u8d5e6\u6b21\uff0c\u6536\u85cf9\u6b21\u3002\u9700\u6c42\u63a8\u8350\u5de5\u5177\u539f\u56e0\u666e\u901a T1 \u8111\u63d0\u53d6BET\uff08\u52a0-R -f 0.4\u5feb\u901f\u3001\u7ecf\u5178T2\u3001PD\u3001\u75c5\u7076\u56fe\u50cfHD-BET\u9c81\u68d2\u3001\u8de8\u6a21\u6001\u3001\u81ea\u9002\u5e94\u8111\u7ec4\u7ec7\u5206\u5272\uff08GM\/WM\uff09\u66f4\u7cbe\u7ec6\u7684\u7ed3\u6784\u5206\u5272\u6279\u91cf\u5904\u7406HD-BET \/ \u81ea\u5199\u811a\u672c\u81ea\u52a8\u5316\u66f4\u9ad8\u3002<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[58,103,3774,86],"topic":[],"class_list":["post-41074","post","type-post","status-publish","format-standard","hentry","category-server","tag-linux","tag-ubuntu","tag-3774","tag-86"],"yoast_head":"\nUbuntu \u5b89\u88c5 FSL \u53ca\u591a\u6a21\u6001\u8111MRI\u7684\u53bb\u9885\u9aa8\u5904\u7406\uff08\u542b HD-BET \u6df1\u5ea6\u5b66\u4e60\u65b9\u6cd5\uff09 - 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