Hi,
I'm not quite sure what the problem is from this description, but if you have not applied any distortion correction (either using fieldmaps and BBR or using topup) then this is likely to be a cause for residual mis-registrations between the FA and structural image.
All the best,
Mark
On 22 Sep 2014, at 19:28, M. alshikho <[log in to unmask]> wrote:
> Hi FSL Experts,
> In order to calculate the mean FA for the right hemispheric white matter I registered a mask (derived from the T1 segmentation) then I used FLIRT as the following:
> I registered my FA map to the T1 using FLIRT then I inverted the transformation matrix, after that I applied the inverted matrix to my mask image using flirt and -applyxfm.
> as a result the overlap between my mask and the FA map is still not complete.
>
> Kindly, Can anybody suggest me any other things that can improve my registration?
>
>
> Thanks in advance
> Mohamad
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