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Subject:

Re: DARTEL results in MNI space

From:

Jonathan Peelle <[log in to unmask]>

Reply-To:

Jonathan Peelle <[log in to unmask]>

Date:

Tue, 4 May 2010 09:03:48 +0100

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Hi Meikei

> I read in p.6 of the "Dartel guide" written by Dr. Ashburner (
> http://www.fil.ion.ucl.ac.uk/~john/misc/dartel_guide.pdf ) that,
>
> "Note that results are not in MNI space, but rather in a coordinate system
> that represents the average shape and size of the subjects included in the
> study."  <-- the results here refer to the results of statistical
> analysis done on preprocessed data (smwrc1*.nii)
>
> And then the next section teaches how to use Dartel to spatially normalise
> to MNI space. I've followed the steps and produced the spatial
> transformation that maps from MNI space to the space of Dartel
> template (Template_6_sn.mat). Then when I'm doing 'Combining deformations',
> I'm not sure what images to choose for the step "Apply to". The guide said
> "specify the images for that subject that you would like spatially
> normalised". But before I entered this whole section about normalise to MNI
> space (section 1.2 of the guide), I had already created smwrc1*.nii for all
> my subjects. So I'm not sure if I should apply this spatial normalisation
> step to the rc1*.nii or mwrc1*.nii created by Dartel or anything else......

The method for normalizing to MNI space described in the DARTEL guide
involves mapping the DARTEL template to MNI space, producing the
Template_6_sn.mat file, as you've done.  So, you would want to apply
that warp to images aligned to the DARTEL template.  The rc* images
are just imported, but not normalized; so you would want to apply it
to any of the warped (w*) images.  (I wouldn't think it would make
much difference if you applied it to the smoothed ones, or applied it
to the unsmoothed and smoothed afterward.)

However, note that in SPM8 there is a "normalize to MNI" option that
will take care of this step, and integrates smoothing as well.  So I
would just use that, unless you have good reason not to.  In this case
you'll select the rc* files and flow fields, and the images get
written in MNI space.



> I'm also wondering if there's any way to interpret the results of the
> statistical analysis that I've already done on the preprocessed data
> (smwrc1*.nii), i.e., to translate this kind of results' coordinates (that
> are not in MNI space) into anatomical names of brain regions? Or the above
> spatial normalisation step is the only way of doing so?

A simple way is to just overlay your results on the DARTEL template,
and use your knowledge of anatomy (along with an atlas) to describe
the regions.  Depending on what you are interested in this is often
sufficient.  That being said, it's a good idea to get things into MNI
space for reporting so that other people have a better idea of your
results.


Hope this helps,
Jonathan

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