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.
|