I agree with Clare here - must be a bug in FAST that it's not carrying
over the -ve voxel dimension (which is part of our old standard way of
defining Tal space). We'll fix that - in the meantime you can use
avwcpgeom to reset the dims easily - but also I agree with Clare that it's
much better to segment the original image not a transformed one.
Cheers.
On Thu, 22 Jul 2004, Clare Mackay wrote:
> Hi Krish,
>
> Sounds like FAST doesn't keep the negative voxel dimension, but one
> thing to consider is that you would probably be better off running FAST
> on your data in their original space then registering the data to the
> template afterwards. The interpolation that happens as a consequence of
> registration won't help with the segmentation, and it's easy to apply
> FLIRT transforms to the segmentations afterwards.
>
> Cheers,
> Clare
>
> ___________________________________________________
> Clare E. Mackay, Ph.D.
> Research Fellow,
> Prince of Wales International Research Centre (POWIC),
> University Department of Psychiatry,
> Warneford Hospital, Oxford. OX3 7JX. UK
>
> tel: 01865 455910 fax: 01865 455922
> OCMR: 01865 221866 / 72
> [log in to unmask] www.psychiatry.ox.ac.uk/powic
> ___________________________________________________
> >>> [log in to unmask] 07/22/04 3:43 PM >>>
> Sorry everyone! This should read:
>
> "it seems as if the Talairach origin is not carried over by **Fast**
> either".
>
> It is Fast that I am having problems with, NOT Flirt.
>
> Krish
>
>
> On 22/7/04 3:17 pm, "Dr Krish Singh" <[log in to unmask]> wrote:
>
> > Just to add to my last post, it seems as if the Talairach origin is
> not
> > carried over by Flirt either.
> >
> > Krish
> >
> >
> >> Hi there,
> >>
> >> I've got myself into some laterality difficulties with negative voxel
> >> dimensions. Let me explain what I did:
> >>
> >> 1) Using flirt I registered a radiological axial volume to the FSL T1
> >> template.
> >> avwhd now reports that this has voxel dimensions of -2,2,2 mm which
> is
> >> correct
> >> I think.
> >>
> >> 2) I took the registered volume generated in the above step and
> passed it
> >> through Flirt to generate segmentation maps. avwhd now reports that
> the voxel
> >> dimensions for the segmented images are 2,2,2 which I don't think is
> correct
> >> as
> >> they should be the same as the input image.
> >>
> >> Is the above behaviour expected? It causes me some problems because
> my
> >> software, mri3dX, assumes that if you overlay one volume on another
> and their
> >> horizontal voxel dimensions have different signs, then it needs to
> flip the
> >> laterality of the overlay. In the case of the above, this is clearly
> not the
> >> case.
> >>
> >> All the best,
> >>
> >> Krish
> >
> > --
> > Dr K.D. Singh
> > Senior Lecturer and Convenor of the Neuroimaging Research Group,
> > Director, MRI Research Centre,
> > Neurosciences Research Institute
> > Aston University, Birmingham B4 7ET, U.K.
> > Tel/Fax: +44 (0)121 [204 3865/3864]/[333 4220]
> > [log in to unmask], http://www.aston.ac.uk/lhs/staff/singhkd/
> >
>
> --
> Dr K.D. Singh
> Senior Lecturer and Convenor of the Neuroimaging Research Group,
> Director, MRI Research Centre,
> Neurosciences Research Institute
> Aston University, Birmingham B4 7ET, U.K.
> Tel/Fax: +44 (0)121 [204 3865/3864]/[333 4220]
> [log in to unmask], http://www.aston.ac.uk/lhs/staff/singhkd/
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe 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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