[Insight-users] EPI Ground Truth

[kavec at messi.uku.fi]

Arash,

I am not sure what is the aim of your work, but (as an MRI physicist) I don't
believe that there exist an "EPI ground truth". Even if you would segment your
k-space and use parallel imaging, your EPIs will be distorted and suffer
intensity loss.

Also, I don't believe that non-rigid registration can recover shape and
intensity of EPIs correctly. B0 field mapping is commonly used for this
purpose.

I would chose other approach to evaluate performance of a non-rigid algorithm.
An object (phantom) with known shape and known deformation, imaged with
modality which doesn't suffer from deformation, such as CT.

Cheers

Citát Arash Jahangir <arash at vije.ca>:

> Hi Martin,
> In a way you are right about this being off topic.  But I believe you are
> wrong about this not being of general interest.  A good chunk of  ITK is
> concerned with registration and many people use it for non-rigid
> registration.  Without ground truth, it is very hard to evaluate the
> performance of these algorithms or applications.  So I believe the topic is
> of interest to the list, even though it is not strictly an ITK subject
> during the design phase (it will be during the implementation phase).
>
> Arash
>
>
> ----- Original Message -----
> From: <kavec at messi.uku.fi>
> To: "Arash Jahangir" <arash at vije.ca>
> Cc: "Insight Users" <insight-users at itk.org>
> Sent: Wednesday, December 21, 2005 4:26 PM
> Subject: Re: [Insight-users] EPI Ground Truth
>
>
> > Hi,
> >
> > you should consider first talking to an MRI physicist in order to confront
> > what
> > you would like to do. It is possible that there are people on this list
> > who
> > could provide you some insight, but I am afraid, it is quite off topic for
> > majority.
> >
> > Martin
> >
> > Citát Arash Jahangir <arash at vije.ca>:
> >
> >> Hi all,
> >> I'd like to generate ground truths for the purpose of evaluating brain
> >> EPI
> >> registration algorithms.  I'd like your feedback and advice about this as
> >> well as any resources on the net you may think are useful to the task.
> >>
> >> 1. One approach is to consider a T2 image as a good proxy for EPI.  The
> >> challenge then is to create a realistic distortion that can serve as a
> >> synthetic EPI.  Obviously the intensity values will not be quite the
> >> same.
> >> So the question here is then:
> >>    1a) Are the intensity variations between T2 and EPI close enough to
> >> make a
> >> warped T2 a good synthetic EPI?
> >>    1b) What is a good approach to create a realistic warp to transform T2
> >> to
> >> EPI?
> >>
> >>
> >> 2)  The second approach is to collect a set of registered EPI-T2 (or EPI
> >> to
> >> any other undistorted MRI image) set that human experts believe are
> >> excellent
> >> registrations.  Then generate a statistical model for the typical warps
> >> that
> >> undistort the EPI images.  Finally use one or more corrected (i.e.
> >> undistorted/registered) EPI images as ground truth and apply the
> >> synthetic
> >> warp to it to get a distorted EPI.  The issues here are:
> >>    2a) Is this a sound approach?  What normalization issues should I
> >> consider
> >> before applying a generic warp field based on statistics on an
> >> undistorted
> >> image to produce a synthetic distorted EPI?
> >>    2b) Is there a database of registered EPI images?
> >>    2c) Are the correction warp fields for those EPI images available and
> >> if
> >> not, how can I recover it
> >>
> >> 3.  I guess I should have asked this first :)  what work has already been
> >> done in this area?  Are there programs or databases the provide warped
> >> and
> >> undistorted EPI ground truths?
> >>
> >>
> >> Any and all feedback is highly appreciated.
> >>
> >> Arash
> >
> >
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