Hi Zoe,
On Fri, 13 Jul 2012 08:24:25 +0200, Marko Wilke <[log in to unmask]> wrote:
>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?
>
If you have exported the segmentations using the VBM8 function that writes affine normalized segmentations no additional normalization to MNI is necessary, because all brains were already affine transformed to MNI. You can use the Dartel toolbox to apply the warpings with modulation but without additional MNI normalization.
Best,
Christian
>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 f�r Kinder- und Jugendmedizin
> Leiter, Experimentelle P�diatrische Neurobildgebung
> Universit�ts-Kinderklinik
> Abt. III (Neurop�diatrie)
>
>
>Marko Wilke, MD, PhD
> Pediatrician
> Head, Experimental Pediatric Neuroimaging
> University Children's Hospital
> Dept. III (Pediatric Neurology)
>
>
>Hoppe-Seyler-Str. 1
> D - 72076 T�bingen, 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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