Hi,
If the only difference in the images is the orientation along the LR axis then you can just ignore this.
Everything inside FSL is built to deal correctly with both "neurological" and "radiological" ordering of the data, and in fact fslreorient2std does not even change this order, but will just maintain the current order. So if all the other axes are the same then just leave everything as it is and continue with your analysis and all should be fine.
There is no need to change the search space.
If you have problems with the registration then let us know, but I can assure you that a change in the sign of the LR axis orientation will not be the cause of any problems.
All the best,
Mark
> On 14 Nov 2018, at 14:08, Josh Robinson <[log in to unmask]> wrote:
>
> 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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