FSL-flirt+fnirt--线性配准和非线性配准

    bet  T1W    T1W_brained  -f 0.3 -R -S -B
    bet DTI/b0 DTI/b0.bet -m -f  0.2 -R      
    fslmath
    fslmaths inputVolume -add inputVolume2 output_volume
    fslmaths   T1   -mul  T1W_brained.nii.gz    T1_brained

    重采样-mrgrid
    mrgrid   FA.nii.gz   regrid   -vox 2   FA_upsampled.nii.gz  -force  #重采样
    mrgrid   IN/dwi_denoised_unringed_preproc_unbiased.mif   regrid   -vox 1.25   IN/dwi_denoised_unringed_preproc_unbiased_upsampled.mif  -force

    mkdir preprocessing
    for SUBJ in $(ls | grep *.nii.gz | cut -d . -f1); do     # 位置
        flirt -in ${SUBJ}.nii.gz -ref ${FSLDIR}/data/standard/FMRIB58_FA_1mm.nii.gz -dof 12 -omat preprocessing/${SUBJ}_indiv2std.mat                ## Affine transform--线性配准
        fnirt --in=${SUBJ}.nii.gz --aff=preprocessing/${SUBJ}_indiv2std.mat --config=FA_2_FMRIB58_1mm.cnf --cout=preprocessing/${SUBJ}_warp_indiv2std.nii.gz --iout=preprocessing/${SUBJ}_instd.nii.gz            ## non-linear transform  --非线性配准
    
    done

    flirt+fnirt
    flirt -in subj_mean.nii.gz  -ref ${FSLDIR}/data/standard/FMRIB58_FA_1mm.nii.gz -dof 12 -omat  subj_mean_indiv2std.mat                                ## non-linear transform
    fnirt --in=subj_mean  --aff=subj_mean_indiv2std.mat  --config=FA_2_FMRIB58_1mm.cnf --cout=subj_mean_warp_indiv2std   --iout=subj_mean_instd

    制作mask --0，或1
    fslmaths T1W.nii  -thr 0.5 -bin T1W_mask.nii.gz
    fslmath

    for SUBJ in ${SUBJ_LIST}; do
    ## Segment GM### Skull-stripping
    bet T1w/${SUBJ} T1w/${SUBJ}_skull_stripped -f 0.3 -R -S -B
    ### Segment T1w into CSF/GM/WM
    fast -t 1 -g -B -b -p -o T1w/${SUBJ}_fast T1w/${SUBJ}_skull_stripped
    ## Register GM to MNI
    ### Register T1w to MNI--先将T1W经过flirt和fnirt配准到FMRIB152，再将分割的GM标准化到MNI152
    flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in T1w/${SUBJ}_fast_restore -omat T1w/${SUBJ}_indiv2MNI.mat
    fnirt --in=T1w/${SUBJ}_fast_restore --aff=T1w/${SUBJ}_indiv2MNI.mat --cout=T1w/${SUBJ}_indiv2MNI_warp --config=T1_2_MNI152_2mm
    ### applywarp to GM and move it into MNI
    applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm_brain     --in=T1w/${SUBJ}_fast_pve_1   --warp=T1w/${SUBJ}_indiv2MNI_warp      --out=T1w/${SUBJ}_fast_pve_1_inMNI &

    #  1. 与标准 FA 图像对齐  #vba脚本       
    mkdir preprocessing     
    for SUBJ in $(ls | grep _FA.nii.gz | cut -d . -f1); do     # 位置     ## Affine transform     
        flirt -in ${SUBJ}.nii.gz -ref ${FSLDIR}/data/standard/FMRIB58_FA_1mm.nii.gz -dof 12 -omat preprocessing/${SUBJ}_indiv2std.mat     ## non-linear transform
        fnirt --in=${SUBJ}.nii.gz --aff=preprocessing/${SUBJ}_indiv2std.mat --config=FA_2_FMRIB58_1mm.cnf --cout=preprocessing/${SUBJ}_warp_indiv2std.nii.gz --iout=preprocessing/${SUBJ}_instd.nii.gz     
    done
    
    flirt -in subj_mean.nii.gz  -ref ${FSLDIR}/data/standard/FMRIB58_FA_1mm.nii.gz -dof 12 -omat  subj_mean_indiv2std.mat                                ## non-linear transform
    fnirt --in=subj_mean  --aff=subj_mean_indiv2std.mat  --config=FA_2_FMRIB58_1mm.cnf --cout=subj_mean_warp_indiv2std   --iout=subj_mean_instd