[Mristudio-users] LDDMM for Hematoma

[susumu mori]

Hi Jeff,

Before you start LDDMM, you have to make sure the linear registration (AIR)
is very good. This is similar to non-liner fitting of a XY plot, which
always requires you to do linear fitting first to get a good initial
estimate of the non-linear fitting parameters.

There are cases when AIR fails often due to high intensity inside or outside
the brains of patients. In this case, changing the contrast, as you did
could be one solution. You can't change the contrast ad hoc for LDDMM but
for linear transformation, it is just an initialization. So, all you want to
do is to bring the two brains as close as possible. So, it's ok to use
different approach for different data. What we often do is, 1) try mutual
information,  2) use landmarks, or 3) do skull strip.

Most important things is, to make sure that the linear transformation is
good. Be careful about the angle of the brain and the brainstem. The
sagittal rotation is one of the most difficult parameters, while X, Y, Z
translation and coronal / axial rotation is usually easy to register. If the
sagittal angle is not satisfactory, you should try different approaches.

Also, we recently start to use 9-mode affine (no shearing) very often, which
is now available in the latest DiffeoMap.

Susumu

On Thu, Sep 8, 2011 at 7:59 PM, Jeff Sadino <jsadino.queens at gmail.com>wrote:

> Hello again DTI Experts,
>
> I have a group of patients that have suffered trauma to the head that I am
> putting through the LDDMM pipeline.  A problem I ran across during AIR in
> DiffeoMap is that since the trauma is causing a hematoma in the B0 image,
> the registration is very poor.  On one subject, I performed DiffeoMap AIR
> using the Mean DWI image and the registration came out pretty good.  I am
> wondering if this is a valid approach to perform AIR registration.
>
> For the LDDMM registration, usually I use the FA and the Trace image to
> drive the Kimap.  However, I think I will get the same poor results.  Should
> I use just the DWI image to drive the LDDMM registration?  There would be no
> need to do "Intensity Normalization" on the DWI image, correct?
>
> Thank you very much,
> Jeff Sadino
>
> _______________________________________________
> mristudio-users mailing list
> mristudio-users at mristudio.org
> http://lists.mristudio.org/mailman/listinfo/
> Unsubscribe, send a blank email to:
> mristudio-users-unsubscribe at mristudio.org
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.mristudio.org/pipermail/mristudio-users/attachments/20110908/09aa9786/attachment-0001.html