Thanks for your help. I am on vacation for the next week or so, but once I get back to work I'll start experimenting with making the Dartel templates (and will probably have more questions).
Dear Jordan,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 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?
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 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]de
http://www.medizin.uni-tuebingen.de/kinder/epn
____________________________________________________