HI - I hate to say it but you almost certainly _don't_ want to be
resampling the funcs "to" standard space but keeping them in func space,
for various reasons - what is it you're wanting to do this for?
Cheers, Steve.
On Wed, 21 Jul 2004, Jack Grinband wrote:
> Hi Christian,
> Of course, I should have checked the FAQ first!!!
> Well, I did as suggested and now the brains are within the FOV. Unfortunately, they are still not
> overlapping very well.
>
> I have two func brains that were successfully registered to standard. I then applied func2standard
> without resampling.
>
> standard FOV=[182 218 182]
> func FOV=[200 200 93.5]
>
> diff = (func FOV - standard FOV)/2
> = [9 -9 -44.25]
>
> To adjust for FOV, I added diff to the x,y,z values of the two func2standard.mats. While they were
> mostly overlapping, they were off by up to 25 mm.
>
> Should I just register all the funcs to one func? Then there wouldn't be any FOV issues.
> thanks,
>
> jack
>
>
>
> >Hi Jack,
> >
> >I think you need to adjust the FOV - details are at
> >http://www.fmrib.ox.ac.uk/fslfaq/#flirt_resample
> >
> >in the FAQ (last paragraph). Hope this helps
> >christian
> >
> >> Hi Mark,
> >> I'm a bit confused about how applyxfm works. I am trying to apply
> >> func2standard.mat to func.img. But when I set the reference image to
> >> func.img (or to hires.img), the resulting image goes off the screen. I
> >> know that the func2standard.mat is correct because I get good
> >> registration when the reference is standard.img.
> >>
> >> If I use the gui to set output size based on voxel dimensions (where the
> >> dimensions are equal to func.img), then I get: AvwReadVolume: Error 0.
> >>
> >> Basically, I would like to take several func.img's, align them with
> >> standard.img but keep them in func.img space. Any idea what I'm doing
> >> wrong?
> >> many thanks,
> >>
> >> jack
>
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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