Hi Maarten,

That extra degree of freedom can hide a lot. Try a 7 dof registration between two different brains and you'll see decent overlap.

I'll try and convince you with one more image. I ran flirt with 7 dof on a skull-stripped epi for sub96591.

Three images are attached.

1. epi aligned to mprage (slice 146)
2. mprage (slice 146)
3. overlay with 50% transparency.

I've put the cross-hair at the edge of the posterior extent of the left lateral ventricle. The cross-hair is displayed for the same coordinate on the epi. Look at the shape of the ventricles and the position of the cross-hair. The overlay looks OK because the extra dof corrects for overall differences in brain size and its hard to see the differences in detail (e.g. shape of ventricles). My sense is that these are two different brains.

anyway, thanks for looking in to this!

cheers,

Brad Buchsbaum