Everyone,
I am trying to register a diffusion image to a T1-structural image. I
have found non-linear distortions in the DWI images and wish to correct
these using FUGUE and then register the B=0 image to the T1 structural.
I was wondering about what the best required steps are for using FUGUE
and I had some questions about the regularisation parameters. I am using
FUGUE to operate on diffusion-weighted EPI images.
Firstly, I just wanted to ask about the best sequence of steps used to
register the field map to the warped data. The procedure that I have
been using so far is:
1. Median filter and regularise field map (FM-Undistorted).
2. Forward warp field map magnitude image to produce (FMMAG-Distorted)
3. Register FMMAG-Distorted to B=0 diffusion image (BZero-Distorted),
and produce T(FMMAG-Distorted, BZero-Distorted).
4. Apply T(FMMAG-Distorted, BZero-Distorted) to the field map
(FM-Undistorted) to register the field map to the BZero image.
5. Unwarp the BZero image using transformed field map in undistorted
space producing (BZero-Undistorted).
6. Register (BZero-Undistorted) to the T1-structural image using linear
registration.
Another option for 2 and 3 is to register the B=0 to the fieldmap
magnitude and then use the inverse transformation to register the
fieldmap to the B=0 image.
Is this the best sequence of steps to use?
My other questions are:
Should you skull strip the fieldmap image (skull stripping the magnitude
image and and applying the brain mask) prior to regularisation?
The other questions I have relate to regularisation of the fieldmap.
Thus far I have used two datasets and I have been using the alignment of
the corpus callosum as a qualitative measure of success. For one dataset
no or little regularisation seems to work best, whereas for the other
dataset I cannot find a parameter set that gives good alignment of the
corpus callosum.
My question is: I have been using the FLIRT cost function output to
gauge which regularisation produces the best registration of the
fieldmap magnitude image with the B=0 image. Is there any other way of
determining the "best" regularisation parameters to use?
Thank you in advance,
Chris Adamson.
--
Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons.,
Monash)
Research Officer
Developmental Imaging, Critical Care and Neurosciences
Murdoch Childrens Research Institute
The Royal Children’s Hospital
Flemington Road Parkville Victoria 3052 Australia
T 9345 4306
M XXXX XXX XXX
E [log in to unmask]
www.mcri.edu.au
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