Hi Mathew
I don't know, whether there is an easy way to restrict the parameter estimates to a given interval.
But, there is a simple way to “freeze” a given set of the affine transformation parameters (e.g. don't use the rotation parameters during the parameter estimation). The Motion and Eddy Current correction tool will do this, it is part of SPM ACID toolbox (artefact correction for diffusion MRI, website: www.diffusiontools.com).
However, the ACID toolbox in itself is still under “construction”. And I am not sure whether it will work on CT data at all. It is made for the situation that all images are acquired during a single run (as is usually the case in diffusion MRI). But feel free to give it a try (and don’t blame me if it does not work:)).
If you try it on your CT data, you should do a rigid-body registration beforehands using the default spm_coreg option.
Best,
Siawoosh
--
Dr. Siawoosh Mohammadi
Post Doctoral Research Fellow
Wellcome Trust Center for Neuroimaging
Institute of Neurology
University College London
12 Queen Square
London WC1N 3BG
United Kingdom
Tel. +44-20-344-84368, (internal ext 84368)
Fax. +44-20-7813-1420
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Gesendet: Mittwoch, 10. April 2013 um 20:11 Uhr
Von: "Mathew Guilfoyle" <[log in to unmask]>
An: [log in to unmask]
Betreff: Re: [SPM] Coregistration with shear
Thanks Siawoosh, that's very helpful
Is there any way of constraining/setting limits on the 12 parameters? e.g. limiting rotation to pi/4 in any direction?
Cheers
On 9 April 2013 20:03, Siawoosh Mohammadi <[log in to unmask]> wrote:
Hi Mathew
Just go the the SPM email list and look for
"SV: [SPM] 12 parameter affine coregistration"
and
"André Ahlgren"
There you will find John's explanation to Andre about exactly this topic:)
Siawoosh
--
Dr. Siawoosh Mohammadi
Post Doctoral Research Fellow
Wellcome Trust Center for Neuroimaging
Institute of Neurology
University College London
12 Queen Square
London WC1N 3BG
United Kingdom
Tel. +44-20-344-84368, (internal ext 84368)
Fax. +44-20-7813-1420
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Gesendet: Dienstag, 09. April 2013 um 20:45 Uhr
Von: "Mathew Guilfoyle" <[log in to unmask][[log in to unmask]]>
An: "[log in to unmask][[log in to unmask]]" <[log in to unmask][[log in to unmask]]>
Betreff: [SPM] Coregistration with shear
Hi, is there any way of using spm_coreg or other function to estimate an affine transform that includes shear rather than just the 6 parameter rigid body transform?
I've looked at spm_affreg but this routine, as far as I can tell, can only apply a least squares cost function as opposed to the richer options in spm_coreg.
I want to register CT scan volumes which may have been acquired with gantry tilt, hence the need for a shear.
Many thanks
Mathew
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