Hi Zoe,
since nobody else chimed in, let me have a stab at this:
> We have a question about an analysis we're running with VBM8 with a
> large (n=89) developmental sample.
I guess that means "children" ? :)
> 1. We created study-specific tissue probability maps using the TOM toolbox
Sounds good.
> 2. We used these in VBM8 with the high dimensional option to segment our
> data and obtain the DARTEL export affine grey and white matter segments
I do not think you need the high-dimensional step here as this will (i)
use the default DARTEL template which you have not yet changed and (ii)
you write out the data affine-only anyway. And (iii), it will take much
longer, but will not really improve the quality of your segmentation,
which is what you are interested in at this step.
> 3. We used the DARTEL toolbox to create a custom template based on the
> GM and WM segments obtained in step 2. This is in study-specific space.
Sounds good.
> We are planning to use this template along with the TOM tissue
> probability maps to segment our data with the Estimate and Write module
> of the VBM8 toolbox. We would like to report results in MNI space to
> facilitate comparison with other studies. First of all, given this, is
> it worth it/optimal to have created a study-specific DARTEL template? Or
> does this just add more processing steps to get to essentially the same
> point as just using the default DARTEL MNI template provided in VBM8?
I have said it before (so I wonder why you did not find it in the
archives :) and I say it again: I think that the value of reporting MNI
coordinates in children is dubious at best, and wrong at worst. There
are such substantial changes that are happening in the brain as part of
both structural and functional development that I think it is simply
wrong to assume that the function of a region can reliably be derived
from its localization in such a volatile environment. If you consider
how variable the brain's layout is even in, say, V1 (see the Eickhoff
and Amunts papers on this), I think it is very optimistic (to say the
least :) to assume that (1) this assumption holds in adults, (2) this
assumption holds in children, (3) this assumption is not changed by
development. All this makes me not report MNI coordinates when doing
fMRI in children anymore. I therefore do not bother transforming to MNI
space, although this is not likely to be much of a pain once you have
implemented it (so my objection is on theoretical, not practical grounds).
> Secondly, assuming it is optimal to have created our study-specific
> DARTEL template, what are the next steps in order to end up with GM and
> WM output files in MNI space? Would we need to use the DARTEL 'normalise
> to MNI space' option, or is there a way to do this using VBM8?
I would think the former, but Christian may have an ace up his sleeve on
this one, too :)
Cheers,
Marko
--
____________________________________________________
PD Dr. med. Marko Wilke
Facharzt für Kinder- und Jugendmedizin
Leiter, Experimentelle Pädiatrische Neurobildgebung
Universitäts-Kinderklinik
Abt. III (Neuropädiatrie)
Marko Wilke, MD, PhD
Pediatrician
Head, Experimental Pediatric Neuroimaging
University Children's Hospital
Dept. III (Pediatric Neurology)
Hoppe-Seyler-Str. 1
D - 72076 Tübingen, Germany
Tel. +49 7071 29-83416
Fax +49 7071 29-5473
[log in to unmask]
http://www.medizin.uni-tuebingen.de/kinder/epn/
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