Hi all,
I am new to FSL and this question must be really basic but I would be very happy if you could help me out..
I am trying to co-register two DTI images on different timepoints non-linearly FNIRT using this command:
bet T3_patient001.nii bet_T3 patient001.nii
flirt -ref T1_patient001_dti_FA.nii -in bet_T3_patient001.nii -omat input_FNIRT.mat
fnirt --ref=T1_patient001_coregistered_dti_FA.nii --in=T3_patient001_coregistered_dti_FA --aff=input_FNIRT.mat --iout=coregistered_FNIRT_patient001_T3toT1
but I get the following error message: Warning, Jacobian not within prescribed range. Prescription is 0.01 -- 100 and obtained range is -0.00756225 -- 8.7192
I also tried co-registering the FA-images at timepoint 1 & 3 and the FA-T2coregistered scans at timepoint 1 & 3. but nothing seems to work...
Since I am new to FSL and am just starting to understand I cannot figure out if the problem is (1) in the input images (FA or bo or FA-T2) or in the FNIRT command.
Every help you could offer is greatly appreciated,
Best wishes,
Brigitte
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