Hi

I have a problem that for a lot of my subjects the automatic coregistration does not work well. I've found that when using a skull-stripped structural image the coregistration works much better. Searching the archives, I've come across this possible pipeline:

> - Reorient data series (functional + structural) based on structural volume
> - If necessary (e.g. subject was repositioned): Additionally reorient the functional series to correct for displacement relative to structure
> (- Slice timing)
> - Realignment
> - Segmentation of the structure (SPM12 Segment or SPM8 New segment to make use of the 6 TPMs)
> - Create a skull-stripped version with Imcalc, e.g. structure * (c1+c2+c3)>.75 seems to make quite a good job on my data
> - Coregistration: reference image = skull-stripped structure, source image = mean, other = the functional series
> - Normalisation: Write: apply the normalisation parameters from segmentation step onto the functional series
> - Smooth

I'm wanting to follow something like this, but I have a couple of questions.

 

When creating the skull-stripped version of the structural image, do I used ms* as the structural images rather than s*.

Do I use coregister (estimate) or coregister (estimate & reslice)?

How would I handle the coregistration when using 2 separate sessions? Do add all the functional images from both sessions to "other" in the coregistration step.

Thanks,

Keri