I think Mark would have to comment as I'm not familiar with b0calc.
Peace,
Matt.
On 11/19/13 1:07 PM, "Louis Shue" <[log in to unmask]> wrote:
>Hi Matt
>
>Thanks for the encouragement.
>
>My main concern at the moment is that the light/dark areas of the two
>fieldmaps are not quite consistent which I suspect is related to point 2
>you listed. Do you have any suggestions on how I can make use of the
>orientation to improve the results? I do have access to the original
>DICOM data.
>
>Regards,
>Louis.
>
>On Tue, 19 Nov 2013 10:37:06 -0600, Matt Glasser <[log in to unmask]> wrote:
>
>>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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