Hi,
I have got what I think are reasonable results, but there are some things that needed to be done.
The big one is that your fieldmap and your EPI are not already aligned (or in the same space).
Hence it is necessary to register them together. This is done as part of the FEAT GUI generally,
but for your images I'm not sure if the FEAT processing will work. I got a registration to work
but it was difficult - having brain extractions for both images would help *a lot* here. So I
recommend that you get a brain extraction (which for mice can't be done with BET as it tends
not to work well, so you'll need to do it manually or find another tool somewhere). Once you've
got a brain extracted image you need to create a warped version of the fieldmap magnitude
scan (using the -w option in FUGUE for the output, the brain-extracted-fieldmap-magnitude
as the -i input, and the fieldmap in rad/s as the --loadfmap input, and I would also create a
mask from the brain extracted fieldmap magnitude and use this with the --mask option).
Once you have the warped version of the fieldmap magnitude image (you may need to check
that your unwarpdir is set correctly so that the warped image looks like the EPI image, in that
it has the same kind of distortion in it) then you need to run FLIRT to register the EPI to this
image. Do this with 6 DOF. Then resample the fieldmap image (rad/s image and the mask)
into the EPI space by applying this transformation to both of these images (using the -applyxfm
option in FLIRT). After all of this you will have the fieldmap images aligned (or in the same
space) as the EPI image and only then can you use FUGUE to try and unwarp the EPI.
If you acquisition had been matched in FOV and resolution to the EPI and the mouse had
not moved in between acquisitions then you could have gone directly to using FUGUE to
unwarp the EPI, but as it is you need to get them aligned first, using the method I've
explained here. Once you've done that you should see it being able to unwarp the distortions
correctly.
All the best,
Mark
On 10 Mar 2011, at 03:48, Van Lee wrote:
> Hi,
>
> Yes it is the phase difference image. The echo time difference is 1.01ms.
>
> I already uploaded the structural image for your reference. The ID is 389174.
>
> Thank you very much!
>
> Best regards,
>
> Van L
>
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