Hi
I am trying to correct EPI distortions in a DWI dataset. Unfortunately I
have no B0 field map or reversed polarity blip acquisitions to estimate
the distortion field, so I cannot use fugue or topup. I am therefore
forced to use image registration methods.
I am currently trying to use fnirt to register the B0 (non diffusion
weighted) image to an undistorted T2-weighted image with the same
contrast. Unfortunately, the EPI distortions cause signal pileup in some
regions, which messes up the contrast matching (in particular around the
anterior temporal lobes). The resultant warped image is pretty messy in
these regions. I explored some paramaters of fnirt. I have tried using
the --intmod=local_linear flag with a high-res bias field. I have also
tried using a higher resolution for the warp. Unfortunatly nothing so
far gives me satisfactory results.
I am considering two new approaches, which I am hoping someone here can
comment on:
1. Is there a way to constrain fnirt so that it only warps in one
direction (i.e. the phase-encoding direction)? In the warped B0 images,
the regions with high pileup veer off laterally. If I can constrain the
algorithm so that non-phase-encoding directions are not warped, I can
prevent this happening and hopefully improve the registration.
2. Is there a way to flatten the image, so that intensities in the
pileup regions are closer to that in the reference (undistorted) T2w
image? I have tried doing tissue segmentation and only taking values
that correspond to the gray and white matter, excluding CSF, (where most
of the signal hyper-intensities occur). This does help the EPI
distortions a small amount, but it also introduces new warping artefacts
throughout the rest of the image (presumably because of the loss of
other structural details critical to calculating the warp for the rest
of the brain).
Any assistance that can be offered would be gratefully achieved. Or if
anyone can point me to references to alternative methods that deal with
this problem, that too will be very helpful.
Many thanks
Mark
--
Dr. Mark Drakesmith
Research Associate
Caridff University Brain Research Imaging Centre (CUBRIC)
School of Psychology
Cardiff University
Park Place
Cardiff
CF10 3AT
Tel: +44 (0) 29 2087 0354
Fax: +44 (0) 29 2087 0339
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