Dear community,
I'm a beginner in DTI and FSL so maybe this question is very trivial but I really struggle with this for weeks now.
We are doing a DTI-tractography study with several participants and want to align our subject-images with the template we use (MNI152), from which we also got the ROIs we do the research on.
At the moment we follow this approach (coming from the FNIRT/UserGuide):
bet T1.nii T1_betted -m -R
flirt -ref T1_betted -in b0_unwarped_brain.nii.gz -dof 6 -omat b02T1.mat
flirt -ref /usr/.../MNI152_T1_2mm_brain.nii.gz -in T1_betted.nii.gz -omat T12MNI.mat
fnirt --in=T1_betted.nii.gz --aff=T12MNI.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm
=> now here we only get an empty "my_nonlinear_trans"-file (no matter if we add the MNI152 as a reference again or change the bet-functions in the beginning), which means that there is nothing to see in fsleyes.
(we would continue by applywarp for registering our ROIs as well)
The question is, what we did wrong, if our approach works like this and if it does, are we right to put the MNI-template as the reference (and not the T1/b0) in the first place?
Thank you so much for your help in advance and wish you all a nice and successful day!
Kind regards,
Marvin (Clinical Cognition Sciences, UK Aachen, Germany)
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