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
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Phone Number: 617-724-2358
Fax: 617-726-7422
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