John is right about needing to have the segmentations before hand;
however, using DARTEL may not be needed depending on the animal you
are studying. It all depends on how convoluted the sulci and gyri are
in the animals you are studying.
That said, you can still use DARTEL in animals (see McLaren et al.
2010). To get the priors and segments for DARTEL and segmentation in
SPM, see McLaren et al. 2009. From these two papers, you should be
able to create priors, use the priors for segmentation in SPM, and
then use DARTEL for normalization.
McLaren et al. 2010 -- Rhesus macaque brain morphometry: a
methodological comparison of voxel-wise approaches
McLaren et al. 2009 -- A population-average MRI-based atlas collection
of the rhesus macaque.
Hope this helps.
Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Tue, Nov 20, 2012 at 3:40 AM, Qasim Bukhari <[log in to unmask]> wrote:
> Dear SPM Experts,
> I m trying to use DARTEL without segmentation (since I m working with animal
> subjects). As far as I have understood is, I did the following steps
> 1. Create Template : Here I input the structural images from different
> subjects. Should these structural images be coregistered with each other or
> not ?
> 2. Normalize to MNI : I input the DARTEL template here, Template_6.nii
> created from the last step. Though I didnt understand why we have to input
> the template_6.nii; what difference would it make if I input template_5.nii
> ?? In the subject flow field, I input u_.... created in the last step. In
> the Images field, I input the coregistered functional images of the
> subjects. I believe I can input functional images of all the subjects at
> once; right ???
> So after this it created one mat file, template_6_2mni.mat. I m not sure
> what this mat file means. What I was looking for was a number of normalized
> images; just like it creates when we do the normal normalization step in
> SPM. Can someone please explain this ?
>
> Thanks a lot
> best regards,
> Qasim
>
> Qasim Bukhari
>
> Research Assistant and Doctoral Candidate
>
> Institute for Biomedical Engineering
>
> ETH and University Zurich
>
> Wolfgang-Pauli-Strasse 27, HIT E22
>
> webpage: http://www.micro.biol.ethz.ch/people/sybukhar/index
>
>
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