(hope you guys don't mind I send this off-list continuation of an
on-list discussion back to the list, it might be interesting for others)
Marko Wilke schreef:
> Hi there,
>
>> Anytime.
>
> Yep, same for me. And while I am completely oblivious of the finer
> points of pulse programming, I agree in so far as
>
No pulse programming required, at least on Philips scanners one can
usually tweak all these paramaters on the console from existing
sequences, when you know what you are doing that is. Wasn't all that hard...
>> But when you, for whatever reason, do have to use substantially
>> distorted EPIs and did not record phase maps my advice would be to
>> not coregister them with T1 at all (it might make matters worse
>> because they simply would not match well). Instead, use the mean EPI
>> and normalize it to the EPI template directly, after which you can
>> apply this transformation to your EPIs.
>
> ... I have also used that approach to normalize EPIs directly.
> Incidentally, I also looked into how unified segmentation would work
> for a mean EPI, which was ok, but not really great. An interesting
> byproduct, though, is the bias correction that you get. I always
> wanted to look at the effect of bias correcting EPIs, but never got
> around to doing it in a systematic fashion. Any experience on your sides?
That's interesting, I am actually trying this with a new dataset right
now. It is high resolution 3T EPI data (2x2x2), eg with considerable
distortion, and besides our time series data concerning a smaller FOV we
also acquired one identically angulated 2x2x2 whole brain EPI. The
contrast in that image is pretty good, it approaches T1 contrast at
1.5T. So for 9 out of 10 subjects it can be used for unified
segmentation normalization. And, importantly, it has the same spatial
distortion as the time series data (because we took grate care the
angulation was identical), greatly improving coregistration.
I am not sure however how well segmetation works on more common spatial
resolution EPI data (eg 4x4x4), I think it is more problematic there.
>
>> To check how much your EPIs are distorted, visually compare your EPI
>> with your T1 (from the same subject) using the 'check reg' option in
>> SPM.
>
> ... or do something like (i1 > thr1) - (i2 > thr2) and be scared by
> the amount of tissue that remains :)
>
> Best,
> Marko
--
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Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
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