[Mristudio-users] theory - registration

[susumu mori]

Hi Julie,

Those are all good questions. Our TheoryAIR routine is now being updated to
provide more controls over which transformation you want to use (currently
Rigid only) and how to combine with outlier rejection (slice rejection or
pixel rejection?). Also, currently you can't save TheoryAIRed data. I hope
that we can release the revised version in this front in July.

As for the iteration, we are still accumulating experiences and want to
welcome any information from users. At this point, I would say 5 usually
works. DtiStudio provides visual interface to judge the improvement in
registration. This is an effective method especially when you have repeated
measurements (so that you can see the subtraction of the two to check the
registration/correction quality). At this point, you should rely on your
visual judgment.

As a matter of fact, almost always, difficulty of automated image quality
check is how to quantify the improvement by registration/correction schemes.
If you can quantify the improvement, we would use such a measure to minimize
during the registration and correction process. In the end, our eyeballs are
the best method for judgment which we can hardly beat.


Susumu

On Thu, Jun 17, 2010 at 7:27 PM, Julie McEntee <jmcentee at jhmi.edu> wrote:

>  Hi Susumu,
>
> I was wondering if you have been able to follow-up on your points in the
> email to Darren (below).
>
> I read the response re: TheoryAir from Hangyi, but it did not indicate
> whether TheoryAir does a regid or affine transform to answer whether or not
> it would be able to do eddy current correction-?
>
> I am able to do the Pixel rejection using Darren’s method and obtain
> results with binary mask & no “Image rejection”; however, I get Image
> rejection after performing TheoryAir- is that expected? How do you determine
> the # of iterations to perform with TheoryAir?
>
> Lastly, if I want to do TheoryAir and Pixel rejection, would I do
> TheoryAir, save DWI + b0 images as REC file, re-load into DtiStudio, and
> then perform Pixel rejection/tensor calculation?
>
> Thanks for your help,
>
> Julie
>
> Julie E. McEntee, MA, CCRP
> Senior Research Program Coordinator
> Department of Psychiatry- Neuroimaging
> Johns Hopkins University School of Medicine
> 600 N. Wolfe St./Phipps 300
> Baltimore, MD 21287
> Phone: 410-502-0468
> Fax: 410-614-3676
>
>
>
> On 5/18/10 10:48 AM, "susumu mori" <susumu at mri.jhu.edu> wrote:
>
> Darren,
>
> You are using the "Pixel rejection" correctly and we have to investigate
> why you are getting "Image rejection" results.
>
>
> 1) Should I run other registration methods such as AIR or MI before
> theory-registratin? Will theory-registration take care of eddy current
> correction?
>
>
> >Theory registration should be used instead of AIR or MI. I have to confirm
> Hangyi if TheoryAIR does rigid or affine. I'll get back to you with this
> respect too.
>
>
>
> 2) What images are changed by theory registration?  The original
> images? It doesn't seem to produce new images such as with mutual
> information or AIR.
>
>
> >Yes, when you use TheoryAIR, you don't get a copy. The original images are
> overwritten.
>
>
>
> Thanks,
> Darren
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