Cibu,
You may try:
0) use standard-orientation-analyze B0 and FA img files
1) normalize B0 to EPI template
2) also apply the warp parameters to FA.
Or you may try our two-step method:
0) use standard-orientation-analyze B0 and FA img files
1) segment B0
2) normalize the white matter segment to white matter template
3) apply the warp parameters to B0 and FA
4) normalize 1st-step warped B0 to EPI template
5) apply the warp parameters to the 1st-step warped FA.
Cheers,
Witaya Sungkarat
> Hello
>
> I am trying to normalize single subject FA volumes on to the T2
> template. I have done this before with spm 2 and the normalization
> worked beautifully.
>
> Now, I am getting badly warped normalization output and would greatly
> appreciate any help with fixing this.
>
> I presumed that the warping may be because of the difference in
> orientation of the FA volume and flipped it along x and y planes to
> correspond with the orientation of the T2 template, which I am told is
> in Neurological convention. But this didn’t help either.
>
> Attached are some pdf files that show:
>
> 1. the original FA volume (we used a vitamin e capsule on the right
> temple area to avoid r/l confusions)
>
> 2. Flipped FA volume (note the position of the capsule shows that
> right is right)
>
> 3. Normalized output.
>
> Please note that I am still using SPM 2.
>
> Looking forward to hearing from you
>
> Cibu Thomas
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