Hello Andrea,

> Christian said that using the Template_6_IXI550_MNI152.nii in the
> High-dimensional option of the Spatial normalization step allows us
> to skip the MNI normalization that is carried out in the original
> Dartel approach. Bc we have a pediatric sample, we ran the create
> Dartel template step with n=100 (we have unequal group sizes, so we
> randomly chose 20 subjects per group to match the n per group of the
> smallest group, i.e., to avoid bias by having unequal group sizes in
> the template: n=52, n=53, n=39, n=20, and n=20).

I am not sure this was the best approach as you could argue that, for 
the smaller groups, subjects are favored as all have contributed, while 
in the larger groups, some have not. This is perhaps a more conceptually 
sound than practically relevant argument, but still, I would have simply 
included all subjects (as just mentioned again yesterday).

> If they are not, what additional steps would you recommend carrying
> out to be able to view our results on an MNI brain and report in MNI
> space?

This is where I seem to have a lack of compassion: why is reporting in 
MNI coordinates critical? If you choose an appropriate underlay (next) 
you should be able to visualize your results in such a way that the 
reader can appreciate size and location. After all the work of Simon 
Eickhoff, Alexander Hammers and countless other colleagues, I am more 
and more reluctant to believe that a number will unambiguously identify 
a region which will then unambiguously tell you the function. I already 
have severe doubts that this is the case for most of the "more 
interesting" (i.e., higher cognitive) regions in the adult brain and am 
even more skeptical when it comes to the developing brain. I may well be 
old-fashioned and I know the argument about meta-analyses, but I am 
still not convinced. It may be convenient, it looks scientific, and some 
journals even require it, but that does not automatically make it a good 
idea for all studies.

> Question2: Marko, I know you recommend NOT interpreting pediatric VBM
> results in MNI space

Yes, but just in case people have not noticed I went at it again :)

>  - what would you recommend as an alternative to
> MNI canonical brains to use as an underlay for viewing our results?
> Would it be the "average" weighted brain output from TOM8 (e.g., we
> get T1_Template_Age13.493.img)? We get this when we input the age and
> sex of our subjects using the "average approach" in: TOM8 > Create
> new template > Write priors/template as single file or multiple files
> > *Priors for SPM8/VBM8 ‘new segment’ (*please note we did NOT input
> any of our T1 images in TOM8, only the age and sex vectors for our
> subjects).

This would be one way but it would be only an age-appropriate template, 
not the age-appropriate template you used for processing. The latter 
would be preferable in my opinion (say, the first volume of the final 
DARTEL-template you ultimately used).

> Question3: We would like to be able to use small-volume corrections
> for a priori regions (amygdala, hippocampus, striatum regions) but it
> is unclear what to use for masks if the answer to Question1 above is
> that our results using a custom Dartel template are NOT in MNI
> space. Do you have any suggestions for alternative masks to use for
> small volume corrections for these subcortical structures?

You could either draw it by hand on the template you used or warp the 
brain underlying the atlas in question to your brain. In the case of the 
Hammersmith Atlas, you could even warp all 30 contributing images and 
compute the intersection of the resulting masks. But again, these are 
adult brains.

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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