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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