Registration flirt & fnirt의 순

Initial Processing 

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/StepByStep

Stand-alone registration can be conducted using first linear (FLIRT) followed by non-linear (FNIRT) registration

FLIRT is an example of a software that performs linear registration, meaning that it will translate, rotate, zoom and shear one image to match it with another. Sometimes the differences between subjects are such that the linear transform is not sufficient to achieve good registration. The local deformations permitted by a non-linear method may then do a better job.

1. 먼저 flirt를 먼저 시행한다. 

/usr/local/fsl/bin/flirt -in /Volumes/SAMSUNG/Dementia_brain_Imaging/2011/10004953_20111116/Structural_MRI/_Volumes_SAMSUNG_Dementia_brain_Imaging_2011_10004953_20111116_Structural_MRI_KIM_EUN_GYEONG_3DT1TFE_SAG_SENSE_6_1.PAR.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -out /Volumes/SAMSUNG/Dementia_brain_Imaging/2011/10004953_20111116/Structural_MRI/T1_templete.nii.gz -omat /Volumes/SAMSUNG/Dementia_brain_Imaging/2011/10004953_20111116/Structural_MRI/T1_templete.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12  -interp trilinear

flirt -in ${f}/brain_fsl.nii.gz -ref ${template}/infant-${2}.nii -out ${f}/registration/brain_to_mni_flirt -omat ${f}/registration/str2mni.mat

2. 다음으로 fnirt를 시행한다. 

fnirt --in=/Volumes/SAMSUNG/Dementia_brain_Imaging/2011/10004953_20111116/Structural_MRI/structure_templete--ref=/usr/local/fsl/data/standard/MNI152_T1_2mm_brain --aff=/Volumes/SAMSUNG/Dementia_brain_Imaging/2011/10004953_20111116/Structural_MRI/structure_templete.mat 

fnirt --in=${f}/brain.nii.gz --aff=${f}/registration/str2mni.mat --out=${f}/registration/str2mni_warp_xfm --config=${template}/infant_${2}.cnf --ref=${template}/infant-${2}.nii

반드시, '='를 삽입한다.