Note that DARTEL normalised brains don't conform to MNI space anyway - unless 
you have taken steps to transform all your warped data from the average 
subject space to MNI space.

If you use the Check reg button, you can see how the mask.img relates to the 
data you are analysing.  Providing the data are in MNI space, and your mask 
corresponds with the nit of data you want to analyse, then there shouldn't be 
a problem.

Best regards,
-John

> The latest statistical analysis that I performed, I used as Absolute
> Threshold Masking of 0.25 with an explicit masking of brainmask.nii, and
> that seems to keep all 'activations' inside the glass brain.
>
> My question is, is this fair to use threshold masking of 0.25? How
> realistically does this map onto the MNI template and MNI anatomical
> coordinates?
>
> On Thu, Nov 13, 2008 at 11:22 AM, Muhammad Parvaz <[log in to unmask]> wrote:
> > Hello Mr. Phillip,
> >
> > I have already normalized all my images and template to MNI space after
> > DARTEL, THEN I smoothed them and THEN I ran my statistics on them and got
> > the results which we discussed in my earlier emails.
> >
> > I still have the same problem, if I overlay it on my mask, the
> > activations seem to be inside the mask, but if I overlay it on the
> > template_6.nii (final template created by DARTEL) which I have already
> > normalized and smoothed, I still get activations outside the brain. What
> > do you think I can (should) do? and how do the coordinates of my
> > 'activations' map on the the anatomy in MNI space?
> >
> > Thanks
> > -M
> >
> > On Wed, Nov 12, 2008 at 5:07 PM, Saemann Philipp 
<[log in to unmask]>wrote:
> >> Complex:
> >>
> >> 1. if you want to use regional assignment tools such as MSU you have to
> >> be sure that you/your template is in MNI space -
> >> so the warped images from DARTEL need to undergo an affine
> >> transformation from DARTEL template space to the MNI template
> >> delivered by SPM.
> >>
> >> 2. Otherwise, you can only visually assess your results by using your
> >> DARTEL template as background; your template is basically
> >> a perfect average of your warped GM maps of all subjects - however, as
> >> indicated this template may have drifted out of the MNI space a bit.
> >>
> >> Also see DARTEL pdf from JOHN where it is explained how to bring your
> >> images back to MNI space.
> >>
> >> Only after this step the MNI coordinates are applying to your data
> >> again.
> >>
> >> vG Philipp
> >>
> >>
> >> Max Planck Institute of Psychiatry
> >> NMR Research Group
> >> Kraepelinstr. 2-10
> >> 80804 Munich
> >> Mail: [log in to unmask]
> >> Phone: 0049-89-30622-413