Dear Richard,
We also see shifts in the z-direction with simple EPI registration.
These are made better by weighting the ventricles, but the best solution
is to use prelude & fugue to unwarp the EPIs and sigloss to calculate
a cost function weight based on the estimated signal loss. However,
all of the latter steps involve the acquisition of fieldmap data.
If you do not have fieldmap data then the best thing to do is to make
a cost function weighting image that does the following:
- de-weight (assign zero) to all areas on the EPI where there is clear
distortion or signal loss (this will involve some subject generation
of the weighting images, which is the trade off for not having
fieldmaps)
- weights the ventricles highly (if these have good contrast)
- in the mid-sagittal slice of the EPI, find the main blood vessels
near the
ventricles (these usually appear dark) and also de-weight these
Note that the fact that blood, and especially large veins, appear very dark
in the EPI but usually not in the structural (due to T2* weighting in the
former) and therefore do not match well. Although the cost functions
correlation ratio and mutual information are somewhat insensitive to
mismatched intensities - small structures like this, which do not heavily
weight the statistics of the whole image, can still cause problems of
mis-registration as the mismatch may be slightly less in the mis-registered
position than in the well-registered position (since neither match well).
In general, the de-weighting of the large signal-loss and distorted areas
in the inferior portion of the brain is the most important step as this
often causes a lot of erroneous shifting in z.
As to the "fix" of add 3.0 to the z translation - I think that may work OK
for images from the same scanner and similar individuals, but I wouldn't
trust it in general. I would definitely advocate trying the above weighting
options (and various cost functions - corratio, mutualinfo, normmi) to
see if you can get the same or better results. And also think about using
fieldmaps in the future.
I hope this is helpful.
All the best,
Mark
Richard Albistegui-DuBois wrote:
> This is a sort of followup to an earlier question of mine, when I was
> looking for ways to improve the registration of a BOLD EPI series to
> a T1 spin-echo structural. The problem ended up being susceptibility
> artifact in the EPI, and weighting the registration toward the
> ventricles improved things.
>
> I have since found that the weighting did not always improve things
> significantly, and seemed highly dependent on very small variations
> in the weighting mask. However, I have found that simply adding 3.0
> to the z-translation component of the affine matrix from the weighted
> transformation produces nearly perfect results.
>
> I am not sure why the weighted transformation would be so good, but
> consistently off by a small distance in Z, but I thought I would post
> this to share the solution I found, and to ask if this behavior is
> normal.
>
> Thanks, all.
>
> -Richard
>
>
> Richard Albistegui-DuBois
> UCLA NeuroRehab, lab of Bruce Dobkin, MD.
> Office: 1-132 Reed
> Phone: 310-825-4016
> Mobile: 310-774-1305
> Fax: 310-794-9486
> AIM: dubistegui
> email: [log in to unmask]
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