Dear Jordan,
Marko's pipeline is exactly doing what you need. However, the las step "iv" is in my opinion not necessary. In VBM8 the accuracy of segmentation is independent from DARTEL steps. DARTEL only helps in obtaining a better spatial normalization. Thus, the last step will not improve your segmentations anymore and DARTEL was already applied.
If you write out the segmentations for DARTEL I would strongly recommend to use the affine transformation as Marko suggested. This step will provide your images after spatial normalization in a space that is close to MNI space. Otherwise, you end up in a sample-specific DARTEL space and you have to transform your images finally to MNI space. The latter approach requires more deformations to adapt for different overall brain sizes, which might be more difficult for children brains.
Regards,
Christian
--
____________________________________________________________________________
Christian Gaser, Ph.D.
Departments of Psychiatry and Neurology
Friedrich-Schiller-University of Jena
Jahnstrasse 3, D-07743 Jena, Germany
Tel: ++49-3641-934752 Fax: ++49-3641-934755
e-mail: [log in to unmask]
http://dbm.neuro.uni-jena.de
On Thu, 5 Jan 2012 09:03:52 +0100, Marko Wilke <[log in to unmask]> wrote:
>Dear Jordan,
>
>> In VBM8 estimate and write we are interested in using DARTEL for spatial
>> normalization, but want to know how this would affect our pediatric
>> sample. We are making our own tissue probability maps, but does using
>> DARTEL still put our brains into MNI space? What is the standard
>> protocol for pediatric brains?
>
>I think the first thing to say is that there is no standard protocol for
>pediatric brains as there is no standard pediatric brain. You will have
>to great lengths to appropriately normalize a baby's brain but will have
>much less trouble with a teenager's brain (at least in that regard :)
>
>In any case, if you want to use the DARTEL'ish approach integrated in
>vbm8, I think you will have to provide an appropriate dartel template
>for this, i.e., one generated from your group or a generic pediatric
>one. What I recently did (rather convoluted, but you asked :) is i)
>generate a TOM template for your study, ii) use that within vbm8 to
>generate initial tissue maps for import into DARTEL (I suggest using the
>affine option here), iii) use DARTEL - generate template to do just
>that, and then iv) use that template within vbm8 to segment the original
>data again and warp it into this template's space. You can also save the
>deformation fields here to take along other images. All of this,
>however, only works if you have a large-enough group, with the 100.000 $
>question being what "large enough" is in the first place.
>
>Re: MNI space, I personally do not care that much about what space it is
>as once I use my own template I am in nobody else's space anyway. And
>even if I go to MNI space, I would still not believe that the
>coordinates that label a certain structure reliably in adults do the
>same thing for a younger child.
>
>Hope this helps,
>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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