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

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