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Pipeline主要步骤
The stages in the pipeline (in order) are:
1 reorient the images to the standard (MNI) orientation [fslreorient2std]
2 automatically crop the image [robustfov]
3 bias-field correction (RF/B1-inhomogeneity-correction) [FAST]
4 registration to standard space (linear and non-linear) [FLIRT and FNIRT]
5 brain-extraction [FNIRT-based or BET]
6 tissue-type segmentation [FAST]
7 subcortical structure segmentation [FIRST]
命令用法
Usage: fsl_anat [options] -i <structural image>fsl_anat [options] -d <existing anat directory>Arguments (You may specify one or more of):-i <strucural image> filename of input image (for one image only)-d <anat dir> directory name for existing .anat directory where this script will be run in place-o <output directory> basename of directory for output (default is input image basename followed by .anat)--clobber if .anat directory exist (as specified by -o or default from -i) then delete it and make a new one--weakbias used for images with little and/or smooth bias fields--noreorient turn off step that does reorientation 2 standard (fslreorient2std)--nocrop turn off step that does automated cropping (robustfov)--nobias turn off steps that do bias field correction (via FAST)--noreg turn off steps that do registration to standard (FLIRT and FNIRT)--nononlinreg turn off step that does non-linear registration (FNIRT)--noseg turn off step that does tissue-type segmentation (FAST)--nosubcortseg turn off step that does sub-cortical segmentation (FIRST)-s <value> specify the value for bias field smoothing (the -l option in FAST)-t <type> specify the type of image (choose one of T1 T2 PD - default is T1)--nosearch specify that linear registration uses the -nosearch option (FLIRT)--betfparam specify f parameter for BET (only used if not running non-linear reg and also wanting brain extraction done)--nocleanup do not remove intermediate files
输出目录
与包含结构像的文件夹<dir_name>同目录下，建立添加名为<dir_name>.anat的文件夹，用来保存命令输出结果。
原始文件 ：T1.nii.gz
旋转和剪切： T1_orig.nii.gz， T1_fullfov.nii.gz
Bias-correction： T1_biascorr.nii.gz
配准： T1_to_MNI_lin.nii.gz (linear registration output)
T1_to_MNI_nonlin.nii.gz (non-linear registration output)
去颅骨： T1_biascorr_brain.nii.gz， T1_biascorr_brain_mask.nii.gz；
分割： T1_fast_pve_0.nii.gz, T1_fast_pve_1.nii.gz, T1_fast_pve_2.nii.gz - partial volume segmentations (CSF, GM, WM respectively)
皮层下分割： T1_subcort_seg.nii.gz - summary image of all subcortical segmentations. All other outputs in the first_results subdirectory.
一个实例
fsl_anat --noreg --nononlinreg --betfparam=0.3 -i mai*.hdr -o ${Source_dir}/data
(资料来源 https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/fsl_anat)
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