Hi,
Before I start it might be useful to reiterate for everyone that:
FLIRT always uses the *reference* volume to determine the voxel
size and FOV (matrix size and number of slices) of the output image.
I don't think you actually want what is described in the message that Steve
referred to. I think you just want to keep the original EPI voxel sizes and
FOV, whilst still applying the rotation/scaling/skews. Correct?
If so, the command you put in is correct. That is:
flirt -in lowres4d -ref lowres4d -applyxfm -init epi2anat.xfm -out
lowres4d_to_t1
As long as lowres4d really is the original EPI, the output should have the
same voxel size and FOV. Is this not the case?
The only problem that can occur when doing this is when the FOV of the EPI (in
mm)
is smaller than the FOV of the highres, so that you get a cropped portion of
the image as the output. If this is your problem then you have two choices.
You can either increase the FOV of the output by making a new dummy
reference volume with EPI voxel sizes but larger FOV, or you can change the
translation parameters in the flirt transformation matrix in order to re-centre
your image in the smaller EPI FOV.
If this doesn't explain what is going on then please give us more details.
All the best,
Mark
> Hi - I think this is answered at
> http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0108&L=fsl&D=0&P=711
>
> but if not I'm sure Mark will add more info.
>
> Thanks, Steve.
>
> On Fri, 8 Feb 2002, Hauke Heekeren wrote:
>
> > Dear FMRIBbbers,
> > I'd like to use flirt to align EPI data with a highres T1 volume
> > and maintain the resolution (number of slices, voxel size) of the original
> > EPI images.
> >
> > I played around with flirt's options but it always resulted in a resampled
> > EPI_aligned.
> > Finally I tried using a dummy ref_volume (actually a copy of t2), like this
> >
> > flirt -in lowres4d -ref lowres4d -applyxfm -init epi2anat.xfm -out
> > lowres4d_to_t1
> >
> > but that didn't do the trick?
> >
> > What am I missing?
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