prefreesurferpipeline学习

# 1. To average any image repeats(i.e. multiple T1w or T2w images available)
# 2. To create a native, undistorted structural volume space for the subject
     * Subject images in this native space will be distortion corrected
       for gradient and b0 distortions and rigidly aligned to the axes
       of the MNI space. "Native, undistorted structural volume space"
       is sometimes shortened to the "subject's native space" or simply
       "native space".
# 3. To provide an initial robust brain extraction
# 4. To align the T1w and T2w structural images (register them to the native space)
# 5. To perform bias field correction

# 6. To register the subject's native space to the MNI space

个体到模板配准（？）

log_Msg "Performing Atlas Registration to MNI152 (FLIRT and FNIRT)"${RUN} ${HCPPIPEDIR_PreFS}/AtlasRegistrationToMNI152_FLIRTandFNIRT.sh \    --workingdir=${AtlasSpaceFolder} \    --t1=${T1wFolder}/${T1wImage}_acpc_dc \    --t1rest=${T1wFolder}/${T1wImage}_acpc_dc_restore \    --t1restbrain=${T1wFolder}/${T1wImage}_acpc_dc_restore_brain \    --t2=${T1wFolder}/${T2wImage}_acpc_dc \    --t2rest=${T1wFolder}/${T2wImage}_acpc_dc_restore \    --t2restbrain=${T1wFolder}/${T2wImage}_acpc_dc_restore_brain \    --ref=${T1wTemplate} \    --refbrain=${T1wTemplateBrain} \    --refmask=${TemplateMask} \    --ref2mm=${T1wTemplate2mm} \    --ref2mmmask=${Template2mmMask} \    --owarp=${AtlasSpaceFolder}/xfms/acpc_dc2standard.nii.gz \    --oinvwarp=${AtlasSpaceFolder}/xfms/standard2acpc_dc.nii.gz \    --ot1=${AtlasSpaceFolder}/${T1wImage} \    --ot1rest=${AtlasSpaceFolder}/${T1wImage}_restore \    --ot1restbrain=${AtlasSpaceFolder}/${T1wImage}_restore_brain \    --ot2=${AtlasSpaceFolder}/${T2wImage} \    --ot2rest=${AtlasSpaceFolder}/${T2wImage}_restore \    --ot2restbrain=${AtlasSpaceFolder}/${T2wImage}_restore_brain \    --fnirtconfig=${FNIRTConfig}