Hello FSL experts,
I am using FDT to process DTI data to do probabilistic tractography. Currently I am FLIRTing the b0 to the subject t1, and then FLIRTing and FNIRTing the subject t1 to a template t1. When using FLIRT and FNIRT for the t1s, I find that my in and ref images have different orientations on the LR axis, as read by fslhd. Heeding the many warnings against using fslswapdim, I was wondering if it would instead be possible to use fslreorient2std on the data? I am hesitant as I would think I would need to reorient the diffusion data as well and this would also require reorienting the bvecs? Is this accurate?
Is it even necessary for this orientation to match? I have read in other threads that FLIRT can *usually* find the right registration even if the orientations do not completely match.
Any help is much appreciated.
Josh
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