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).

Also, there are two Jordans emailing the listserve. But... we share an office. 

Thanks!
Jordan Constance

On Thu, Jan 5, 2012 at 2:03 AM, 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 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
____________________________________________________



--
Jordan Constance, B.S.
Graduate Research Assistant
Child Clinical Psychology
Southern Illinois University Carbondale