Hi
within FSL you'd normally use flirt to do this kind of thing. All you need
is to create a 4x4 matrix in a text file and pass this to flirt with the
-init -applyxfm option. An example would be
1 0 0 0
0 -1 0 (FOV Y)
0 0 1 0
0 0 0 1
if you want to flip around y. Mark Jenkinson has explained this in more
detail in an email to the fsl list on the 21. Nov 2001
WRT your second question: FSL does not yet come with an interactive
display utility. For this kind of thing, we recommend tools like Krish
Singh's mri3dX, mricro, 3D visionworks, MEDx etc
Within fsl, the three tools available are
slices, which gives you a 3x3 array of views : try slices example
slicer, which creates a graphics file that can then be viewed using
display
overlay, which allows you to overlay one image onto another
I'm surprised that display does not seem to work for you, how are you
using it?
ta
Christian
Christian F. Beckmann
Address: Oxford University Centre for Functional
Magnetic Resonance Imaging of the Brain,
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
Email: [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann/
Phone: +44(0)1865 222782 Fax: +44(0)1865 222717 Mob: +44(0)7980 691852
On Sat, 13 Jul 2002, Darren Weber wrote:
> Hi Andy,
>
> what is the slice orientation of the analyze files - axial, sagittal,
> coronal? Which of these orientations is the y direction?
>
> The default Analyze volume is radiological orientation, that is +XYZ = RAS
> (right, anterior, superior).
>
> Maybe you can use AIR to flip the volumes, just in Y.
>
> If you use mricro and AIR, you could evaluate the orientation problem for
> one EPI volume and then develop a script to apply it to all of them.
>
> Kind regards, Darren
>
> PS, My apologies to the FSL team for butting in. You can probably do this
> stuff with avwutils?
>
>
> ----- Original Message -----
> From: "Andy Goldfine" <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Saturday, July 13, 2002 6:21 AM
> Subject: [FSL] image flipping
>
>
> > My EPI images (from GE then converted to ANALYZE and then a hdr created
> > with avwcreatehd) have the y orientation backwards making registration
> > impossible. Is there a way to flip the y axis of images?
> >
> > Secondly, FSL is missing an image display utility like in SPM. How do
> > you recommend displaying images to see how they look and also to do
> > orientation. "display" doesn't seem to work and "slicer" seems
> > difficult.
> >
> > Thanks
> >
>
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