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Subject:

Re: shift in B0 unwarping

From:

Doug Greve <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Mon, 22 Nov 2004 20:41:29 -0500

Content-Type:

TEXT/PLAIN

Parts/Attachments:

Parts/Attachments

TEXT/PLAIN (116 lines)

Thanks Mark, that's just what I was looking for.

doug


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,
>       Mark
>
>
>
>
>
> 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
>> voxels
>> 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?
>>
>> thanks
>>
>> doug
>>
>>
>>
>> --
>> 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.
MGH-NMR Center
[log in to unmask]
Phone Number: 617-724-2358
Fax: 617-726-7422

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