Dear Karin,
If your 29 slices cover a reasonable amount of the brain anatomy then
you might just be able to use the 29-slice fieldmap and get everything
to work fine inside of the standard FEAT GUI. So try that first.
If that does not work then it would be best if you had a wholehead EPI
as well (with the same parameters as your 29-slice version) so that it
was possible to register these two EPIs together, get the fieldmap
applied to both and then proceed with your unwarped versions inside
FEAT.
The main problems with partial field of view acquisitions is getting the
registrations to work, but if that will work with the standard processing
then you are fine. Otherwise, the alternative will probably require
some manual command line use of FLIRT and FUGUE.
Let us know how you get on.
All the best,
Mark
On 27 Jan 2011, at 01:45, Karin Cox wrote:
> Hello,
>
> I am preparing to use FUGUE on a set of 29-slice functional EPI volumes that cover only a limited extent of the brain. I have collected two sets of fieldmap data: 29-slice magnitude and phase images that correspond to the same slices included in the fMRI volumes, and 51-slice magnitude and phase images that include both the original 29 slices as well as additional slices above and below to ensure full brain coverage. What is not clear to me is which set of fieldmap data I should use in FUGUE. My best guess was that I should use the 29-slice fieldmap data, but I thought that I would check and see if this was indeed the case.
>
> Thank you,
> Karin
>
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