Dear FSL-experts,
I am trying to register the DTI scans (FA and MD) of a subject to the FMRIB58_FA_1mm-standard.
I did this with the commands :
flirt -in dti_FA -ref ${main_dir}/FMRIB58_FA_1mm.nii.gz -out dti_FA_reg
flirt -in dti_MD -ref ${main_dir}/FMRIB58_FA_1mm.nii.gz -out dti_MD_reg
The registration of the MD image works fine (more or less), but for the FA image, the sagital and the axial plane have swapped place after the registration.
Is there a way to fix this problem, and is it even a problem if I want to do ROI analysis between subjects afterwards ?
Best regards and many thanks,
Julian Klug
Operating system : Mac OSX 10.11.6
FSL Version : 5.0.9
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