Hi,

I may have a suggestion for this problem.

The problem is that the registered b0 image was not matched to the T1? In the flirt, you could try -searchrx -searchry -searchrz and change the default setting from "-90 90" to "-180 180".

I hope it could work.

Best 

	Szhang

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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