Hi Susie, I have a tool that works very well on this type of thing, but I am not quite ready to release it (a few more weeks). It will be greatly facilitated if you acquired a whole-brain image during your scan (this can include the MPRAGE itself). If not, then you'll have to do some hand registration to get it close (if you collect more data of this type, make sure to get a whole-brain scan -- virtually anything will do, including a single time point from an epi).
doug
Susie Heo wrote:
Hello, I would like to register a 2D EPI oblique axial slice to a 3D MPRAGE and am hoping that Freesurfer will help me do this. I have not had any luck with other fMRI software packages. Caveat: Each subject's EPI axial slice was taken parallel to his/her specific hippocampal longitudinal axis and the angle is unknown. Therefore, I have a low-res 2D axial slice at an unknown angle and a high-res 3D MPRAGE.
Is Freesurfer capable of finding and applying the appropriate transformation? Specific suggestions would be greatly appreciated.
Best, Susie
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