I am trying to register maps of different subjects that are in diffusion space into common MNI space. I am following the code in FSL guide section “Subject to Standard Space Registration”. There is a first step with linear registration where you register the dwi image with b=0 to T1 space using flirt; then you should register T1 weighted image to MNI space first using flirt and then using fnirt (I paste the code of this last point):
flirt -in T1_brain.nii.gz -ref $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz -dof 12 -out T1toMNIlin -omat T1toMNIlin.mat
fnirt --in=T1.nii.gz --aff=T1toMNIlin.mat --config=T1_2_MNI152_2mm.cnf --iout=T1toMNInonlin --cout=T1toMNI_coef --fout=T1toMNI_warp
In the end I should concatenate trasformation matrix from b0 to T1 weighted image with the trasformation matrix from T1 weighted image to MNI space and apply this matrix to the dwi maps.
However, how can I know fnirt trasformation matrix ? The fnirt command does not have a “omat” option…
I thank you in advance.