图像配准之一二三

1. 基于FSL flirt

    在flirt中，cost function {mutualinfo,corratio,normcorr,normmi,leastsq,labeldiff,bbr}  (default is corratio)。分析的数据是single-shell data and one b0，DWI配准受损失函数cost function 影响较大。通过调整损失函数，可改变DWI图像配准方向。参考b站视频。

flirt.fsl -dof 6 -cost normmi -ref T1.nii.gz -in b0_denoise_bias.nii -omat T_fsl.txt

transformconvert T_fsl.txt b0_denoise_bias.nii T1.nii.gz flirt_import T_DWItoT1.txt

mrtransform -linear T_DWItoT1.txt dwi_denoise_preproc_bias.mif align.mif

2.基于基于FSL flirt BBR 

    Boundary-Based Registration (BBR)损失函数，需要FSL FAST生成的白质模板作为边界参考。参考网页：https://community.mrtrix.org/t/registration-of-structural-and-diffusion-weighted-data/203/17

flirt -in b0_denoise_bias.nii -ref T1.nii.gz -dof 6 -cost bbr -wmseg wm_pve_2.nii.gz -omat T_fsl.txt

transformconvert T_fsl.txt b0_denoise_bias.nii T1.nii.gz flirt_import T_DWItoT1.txt -force

mrtransform -linear T_DWItoT1.txt dwi_denoise_preproc_bias.mif align.mif

3. MRtrix Tutorial #6: Creating the Tissue Boundaries

参考网页：https://andysbrainbook.readthedocs.io/en/latest/MRtrix/MRtrix_Course/MRtrix_06_TissueBoundary.html

mrconvert T1.nii.gz T1.mif

5ttgen fsl T1.mif 5tt_nocoreg.mif

mrconvert 5tt_nocoreg.mif 5tt_nocoreg.nii.gz

# Grey Matter segmentation
fslroi 5tt_nocoreg.nii.gz 5tt_vol0.nii.gz 0 1 

mrconvert mean_b0.mif mean_b0.nii.gz

flirt -in mean_b0.nii.gz -ref 5tt_vol0.nii.gz -interp nearestneighbour -dof 6 -omat diff2struct_fsl.mat

transformconvert diff2struct_fsl.mat b0.nii.gz 5tt_nocoreg.nii.gz flirt_import diff2struct_mrtrix.txt

mrtransform -linear diff2struct_mrtrix.txt dwi_denoise_preproc_bias.mif align.mif -force

    分析总结，实践数据为single-shell and one b0，上述三种方法可能不能把所有DWI数据都配准，方法1计算所需时间最短，方法3步骤多，方法2需要FAST处理T1数据。相对来讲，采用方法1，调整不同损失函数可使得DWI数据与T1数据配准。