> Hi,
>
> for an fMRI series which does not cover the whole brain (e. g. 20 slices 4 mm
> thick), how is spatial normalisation best achieved?
>
> Can object masking (be recommended, e. g. a binary mask of the volume) to keep
> the influence of the missing parts and the border zones low ?
>
> Should the starting position be optimized manually (SPM2)?
>
> (Coregistering on T1 did not work properly using MI, otherwise we would have
> used this option)
>
> Grateful for any hints on this,
>
> Philipp
Hi Philipp,
I was advised to do the following with my data:
In CheckReg reset the origin of the functional, so it vaguely the same as
that of the anatomical. Now your co-registration should work and finally
you can normalise, whereas you should change the normalize defaults for
estimation to use heavy regularisation (this should mean that your original
image should not look too different to the normalized image, i.e., the edge
where the brain is cut off stays crisp. You can also change the write
defaults to use a smaller bounding box, so your image size is smaller, but
that's just to save disc space.
I don't know about object masking, maybe someone else can comment on this.
Happy normalizing,
Jane
|