Hi,
Sorry I haven't replied sooner but I haven't tried this before so I
needed
to have a close look at the code. Unfortunately, there is a place in
the
code where it assumes the field map and EPI are the same size so you
can't simply use it as you'd like for now. I will update the code to
make
it more flexible and the next release (probably in a few months' time)
will have this new version.
In the meantime the easiest work around is to down-sample your
field maps to make them 64x64. I know this isn't ideal but it is easy
to do and will work pretty well. To do the down-sampling just use
flirt with something like:
flirt -ref epi -in fmap -out fmap64 -applyxfm
This applies a small blurring prior to applying the transformation in
order
to maintain information from all voxels in the down-sampling, and will
output
a fieldmap (fmap64) which is the same size as the epi, without any
spatial
transformation (the default transform for -init is the identity
transformation).
Then use fugue with the epi and fmap64.
Note that flirt doesn't work with complex images, so make sure
the fmap image used above is either the output from fugue with
the --savefmap option, or the output from prelude.
Also note that it assumes that the images fmap and epi are registered.
Ideally you should down-sample, forward warp the magnitude image
from the field map sequence, register this warped image with the epi
and then apply the transformation to fmap in order to have it properly
registered with the epi. See the information at
http://www.fmrib.ox.ac.uk/fslcourse/flirt_fugue
for more on this.
Hope this does the trick for now.
All the best,
Mark
On Thursday, June 3, 2004, at 08:53 pm, Tom Liu wrote:
> Hi,
>
> We are starting to look at the use of PRELUDE and FUGUE for
> unwarping of DICOM EPI images off a GE 3T short bore, and had
> a quick question: How does FUGUE handle higher resolution field maps?
> e.g. if we acquire 128x128 map, will FUGUE properly apply it to a
> 64x64
> EPI image? Our initial tests seem to indicate that it sort of works,
> but I haven't
> seen anything in the documentation or lists indicating that it should.
> The reason I ask is that the standard SGPR that we're planning
> on using seems to have a silly lower limit of 128x128, and we'd rather
> not
> modify the product code unless we have to.
>
> Thanks,
>
> Tom Liu
>
> ***********************************************************
> Thomas Liu
> Center for Functional Magnetic Resonance Imaging
> University of California, San Diego
> 9500 Gilman Drive, Mail code 0677
> La Jolla, CA 92093
> Phone: (858) 822-0542
> Fax: (858) 822-0605
> http://fmriserver.ucsd.edu/ttliu
> ***********************************************************
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