Hi,
You need to check more than just whether the images are stored radiologically or neurologically (which is what fslorient returns). The best thing to check would be to view the images in FSLview and check that there are no major changes in orientation (e.g., more than 45 degrees out) between any of the image inputs.
All the best,
Mark
> On 27 Feb 2017, at 16:00, Susanne Rubon <[log in to unmask]> wrote:
>
> Dear FSL experts,
>
> I ran a two sample t-test with FLAMEO to test for group differences and thresholded with easythresh afterwards. I also computed a onsesample t-test (also in FLAMEO) with behavioral covariate. When I want to threshold the onesample t-test (with easythresh) using the cluster mask from my two sample t-test, I get the following warning:
> WARNING:: Inconsistent orientations for individual images in pipeline!
> Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
>
> I checked the orientation of both images using fslorient (neurological) and everything looks fine to me in FSLView. Is there something else I should check (also with fslorient)? What could be the reasons for this warning in my case?
>
> Thanks a lot!!
> Susanne
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