Thanks Mark, that's just what I was looking for.
On Sun, 21 Nov 2004, Mark Jenkinson wrote:
> Hi Doug,
> My understanding of the theory is that the registration in
> step 7 should account for the shift as well as any rotations,
> etc. The tricky thing is that there are two reference frames to
> consider: the undistorted-fieldmap-frame (UFF) and the
> distorted-fieldmap-frame (DFF). Now since the EPI is acquired
> in some other frame, it is necessary to register it to the
> fieldmap frame. Since the actual fieldmap acquisition is in
> the UFF, this isn't suitable for registering the EPI, as it
> is distorted. Hence the forward warp creates a distorted
> fieldmap image in the DFF. If there is a mean offset in the
> fieldmap then the DFF and UFF will be offset by a global
> translation, as well as the local distortions. However, if
> the EPI is registered correctly to the DFF, then the process
> of unwarping it, which creates a blank image in the UFF and
> does (reverse) coordinate look-ups in the DFF to move the
> EPI intensities back to the UFF, should correctly account for
> the global shift.
> Now, that's the theory. In practice there may be implementation
> issues with the forward warp so that it isn't a true inverse
> of the required undistorting transformation. So if you are
> finding problems in practice then it may be because of this,
> although I thought that this should work OK still. You can test
> this by trying to unwarp your distorted fieldmap image and
> see if it returns to the correct location, undoing any global
> shift. I think it should, although I'm not sure I've actually
> tested this case.
> To be even more pragmatic - as no-one cares about the global
> shift - then it is perfectly safe to demean the fieldmap as
> soon as it is reconstructed (after step 4) and always use
> the demeaned fieldmap/shiftmap. By doing this you probably
> get more intuitive behaviour, so by all means go ahead with
> this plan if you like. The easiest way to demean would be
> to use avwstats to calculate the mean (over non-zero voxels)
> and then subtract this from the image using avwmaths (remembering
> to re-mask the result).
> Hope this makes sense, and let me know if there does seem
> to be an implementation problem in getting the same image
> back from forward-backward warping.
> All the best,
> On 19 Nov 2004, at 19:01, Doug Greve wrote:
>> Hi Y'all,
>> I've come across an extra step that I need when using the B0 unwarping.
>> Here's what I do now:
>> 1. Create a brain mask from the mag volume (BET)
>> 2. Create a head mask by dilating the brain mask (AVWMATHS)
>> 3. Rescale the phase image to -pi to pi (AVWMATHS)
>> 4. Unwrap the phase (PRELUDE)
>> 5. Create the voxel shift map (VSM) (FUGUE)
>> 6. Forward warp the mag volume (FUGUE)
>> 7. Register the forward warped mag with the example func (FLIRT)
>> 8. Resample the VSM into EPI space (FLIRT)
>> 9. Dewarp the EPI (FUGUE).
>> The problem is that the VSM has a non-zero global mean (about 2.5
>> in one case) due to the fact that we acquired the field map at the end
>> of the session, which was about 1.5 hours after the shim was done. The
>> net shift comes from the fact that the B0 shifts due to heating of the
>> shim magnets.
>> The problem is that the mag is shifted as part of the forward warp and
>> so this shift is not accounted for in the registrtation (step 7), which
>> means that the VSM does not get mapped to the right place (step 8).
>> I have a fix for this which is simply:
>> 5.5 Remove the global within-brain mean in the VSM
>> Would you agree that this needs to be done?
>> Is there something in fugue which will do this? Or is there some series
>> of avwmaths commands which would work?
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> [log in to unmask]
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
Douglas N. Greve, Ph.D.
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Phone Number: 617-724-2358