On Monday, August 29, 2011 10:35:59 you wrote:
> Hi Jesper,
>
> Thanks for your response. I am basically trying to use the AAL Atlas
> parcellation scheme for tractography on FA maps that have been normalized
> to the FMRIB58 1mm template. However, the AAL Atlas is defined in the 2mm
> T1 template and I can't open it on the 1mm FA or T1. Originally, I was
> thinking that I could flirt and fnirt the 2mm T1 template to the 1mm FA
> and then apply the resulting warp to the AAL Atlas. However, if you're
> saying that fnirt is unnecessary and that I shouldn't normalize between FA
> and T1 templates, would I be better off simply flirting the MNI152 T1 2mm
> template to the MNI152 T1 1mm template and then applying this warp to the
> atlas so that I can use it for tractography?
>
> Thanks in advance,
> Anna
Dear Anna,
I'm not entirely sure what you are trying to do, but the FMRIB58 template has
the same field of view as the MNI152 template. The reason you cannot open a
volume sampled at 2mm in MNI152 on an 1mm FMRIB58 template is purely because
the voxel resolution is different (2mm vs 1mm). No transformation is needed to
fix this -- only a resampling. Either resample your 1mm volume at 2mm or
resample your 2mm volume at 1mm using flirt. For example:
flirt -ref my_2mm_template -in my_1mm_volume -out now_its_2mm -applyisoxfm 2
or
flirt -ref my_1mm_template -in my_2mm_volume -out now_its_1mm -applyisoxfm 1
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