According to the explanation in page (FLIRT/UserGuide - FslWiki), I use epi_reg to map DTI(b=0) image to T1 image. My code is as follows:
epi_reg --epi=EPI IMAGE --t1=T1 IMAGE --t1brain=T1 BRAIN IMAGE --out=epi_reg
However, after execute it successfully, I got epi_reg.nii.gz and two mat files: epi_reg.mat and epi_reg_init.mat
Although the epi_reg.nii.gz maps T1 image well, I don’t know how to deal with the two mat files.
I tried to use flirt -ref T1 BRAIN -in EPI IMAGE -init epi_reg.mat(or epi_reg_init.mat) -out dwi2T1
But the dwi2T1 image is different with epi_reg.nii.gz and far from the T1 Brain image.
I have this question, because in my project, I need to map the template to T1 image, then to DTI image. I need to inverse the mat file. But at first I should make sure the mat file fit well.