Dear Dr Watson,
> I am currently trying to align fMRI to T2 images for a neonatal dataset. However I am consistently getting an alignment mismatch which manifests as an 'elongation' in the fMRI realigned images. This appears along the anterior-posterior axis i.e. frontal and occipital regions of the fMRI extend beyond the limits of the structural T2s. Has anyone got suggestions to fix this?
its elementary really. I don't think this is something that is caused by the flirting. It sounds like what you are seeing is distortions in the EPI data which are usually along the y-direction and which lead to an elongation or a compression in the A-P direction depending on the details of your sequence. The solution is to acquire fieldmaps along with the EPI data which will allow you to correct these distortions.
Jesper
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