Sorry, meant to say cubic instead of isotropic - would you recommend
using cubic voxels? Any guidelines for optimum dimensions to use?
Thanks again,
Alex
-----Original Message-----
From: Tim Behrens [mailto:[log in to unmask]]
Sent: Sunday, August 15, 2004 4:55 PM
To: [log in to unmask]
Subject: Re: [FSL] FLIRT in FEAT
No - you don't need isotropic voxels, but you do need the "voxel
dimensions" information in the analyze header to reflect the true
dimension of the voxels in "brain space".
To look at the voxel dimensions in the analyze file do e.g.
for x:
avwval filename pixdim1
for y:
avwval filename pixdim2
etc..
to change voxel dimensions, use
avwchpixdim <filename> <newxdim> <newydim> <newzdim>
hope this helps ...
Tim
------------------------------------------------------------------------
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Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
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On Sun, 15 Aug 2004, Fornito, Alexander wrote:
> Hi, thanks for your quick response! Just to clarify:
>
> "If either of the images looks "compressed" in any axis compared with
the
> othe axes then that means that your voxel dimensions are wrong - it is
> important to fix this in the header before proceeding with
registrations."
>
> What do you mean by "voxel dimensions are wrong"? Do the voxels need
to be isotropic before being fed into flirt?
> Can you give me an example of how I might change the hdr info?
> Thanks again,
> Alex
>
> -----Original Message-----
> From: Stephen Smith [mailto:[log in to unmask]]
> Sent: Sat 8/14/2004 7:41 PM
> To: [log in to unmask]
> Cc:
> Subject: Re: [FSL] FLIRT in FEAT
>
>
>
> Hi Alex,
>
> On Sat, 14 Aug 2004, Alex Fornito wrote:
>
> > Hi all,
> > I have axially acquired epis that I'm trying to register to
the template
> > via coronally acquired T1 structurals (via FLIRT in FEAT) and
have a
> > couple of questions:
> >
> > 1 - I'm using a wholehead epi acquired during the same session
as the
> > initial highres. This is because, although our task epis were
supposed to
> > be wholehead acquisitions, some of the superior-most slices
appear to be
> > chopped off. Should I use 3 or 6 DOF?
>
> Assuming that the time series EPI data is a subset of the
whlehead epi,
> and that there is no chance of rotation between them then DOF=3,
i.e,
> translation only. However it sounds like you have a reasonable
> field-of-view with the time series data, so if there is any
rotation, then
> DOF=6 should work ok.
>
> > 2 - I've used mricro to change the orientation of the coronal
T1
> > structural to be the same as the axial epi. However, I've
noticed the
> > FLIRT FAQ page says the following:
> > "Check that the input image looks fine and that the voxel size
is correct
> > by (a) looking at the images with slices (none of the views
should look
> > squashed or stretched) and (b) checking the voxel dimensions
(pixdim) with
> > avwhd (Note: voxel size can be fixed using avwchpixdim)".
> > If I view my epis and T1s as they are, the sagittal and
cornoal views are
> > compressed in the epis, and the axial and sagittal views are
compressed in
> > the T1s. Does this mean that I need to re-slice the epis and
T1s into
> > cubic voxels before registering them?
>
> If either of the images looks "compressed" in any axis compared
with the
> othe axes then that means that your voxel dimensions are wrong -
it is
> important to fix this in the header before proceeding with
registrations.
>
> Cheers, Steve.
>
> 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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