I agree those files look impressively similar. Some other things that
will influence field maps:
1) b0 shimming
2) Orientation of the head in the b0 field
3) b0 inhomogeneities due to tissue differences other than air/non-air
Have you compared your EPI to T1w registrations with and without your
synthetic field maps yet? Perhaps you are already a lot closer than you
were initially. I wouldn't let a desire for perfection get in the way of
a major improvement. I would imagine a lot of people have data for which
they neglected to acquire field maps but wish to register them more
accurately to their structurals and would be interested in your progress
with this.
Peace,
Matt.
On 11/19/13 5:26 AM, "Louis Shue" <[log in to unmask]> wrote:
>Dear all,
>
>A few months ago, I started looking at the problem of fieldmap-based
>unwarping of EPI when the usual fieldmap sequences (phase-difference
>volumes) were not available. With lots of help from Mark I was able to
>eventually come up with what seemed sensible-looking fieldmaps.
>Essentially the steps I used was
>
>- Extract from T1 a mask to differentiate between air and "everything
>else", i.e. skull+brain+CSF
>- Use b0calc to estiamte the magnetic field variations
>- Scale by 2*pi* gyromanetic ratio
>- Remove spherical harmonics from the resulting volume
>
>Unfortunate after comparing fieldmap determined from this approach with
>fieldmap computed using conventional methods (we were able to acquire
>newer data), there are noticeable differences between the fieldmaps as
>seen in the two files linked below.
>
>Fieldmap computed from phasemap https://db.tt/57Lb8HzM
>Fieldmap computed from T1 volume https://db.tt/Ygte0Zh2
>
>Since we still have substantial data that we would like to process as
>much as reasonably possible, hopefully we can still get something using
>the T1-b0calc approach? I'd really appreciate it if someone can suggest
>where I might be able to improve or where problems might have occurred in
>the above description?
>
>Thanks very much!
>
>Regards,
>Louis.
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