After I preprocessed all my subjects. I’m trying to align my dwi data to the t1.
I did that following the steps from the tutorial but it’s not giving me any good results. I’m hoping I did something very simple wrong and I’ve been trying to figure out the problem, but so far no success.
What I did:
flirt -in mean_b0.nii.gz -ref T1.nii.gz -interp nearestneighbour -dof 6 -omat diff2struct_fsl.mat
transformconvert diff2struct_fsl.mat mean_b0.nii.gz T1.nii.gz flirt_import diff2struct_mrtrix.txt
mrtransform T1_5ttgen.mif -linear diff2struct_mrtrix.txt -inverse T1_coreg.mif
I extracted the mean_b0 from the preprocessed dwi image and I’m trying to align the 5ttgen (which I got from the T1 image).
The result I get:
As you can see, not very well aligned
I’m hoping someone can tell me where I’ve went wrong …