Hi - it sounds like you are just wanting to correct for overall
scaling, so the _only_ numbers you need from the avscale output is
the product of the 3 scalings - this is given on the line entitled
"determinant". Just take this number to achieve your modulation of
intensities.
Steve.
On 28 Feb 2007, at 02:24, Russell Chu wrote:
> Hello everyone,
>
> I've been using 12 dof registrations to register my T1 images to the
> reference MNI image space and would like to know how I can regain
> spatial
> information (lost from scaling and skewing) from the skewing
> parameters
> obtained from avscale. To clarify the problem, here's a brief
> description of
> my main goal:
>
> I would like to create a parital volume map of the gray matter in
> various
> regions of interest in MNI space. If each subject's ROI was simply
> registered to the standard brain, they would all contribute to
> equal amounts
> to the partial volume map. What we need is a way to adjust the
> intensity of
> each voxel in each subject's ROI so that they only contribute to
> the map
> according to their true weights. For example, if one subject's
> brain is
> scaled up by 5% in the registration, I would scale the intensity of
> every
> voxel in that image by multiplying the entire image by 1/1.05.
> However, I
> don't know how I could factor skews into that.
>
> My first roadblock is that I don't understand what each of the skews
> represent (xy, xz, yz). Does anyone know how these values affect
> each pixel
> in the image?
>
> Thanks in advance,
> Russell
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Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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