Hi,
>
> 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?
Exactly.
>
> 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?
They are the same and do have same voxel size and FOV.
>
> 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.
That makes sense, they do have different FOVs and the resulting image is
cropped. I'm going to try what you suggested,
Thanks,
Hauke
> 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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