[Mristudio-users] co-registration question.

[susumu mori]

Hi Jan,

First of all, please make sure the following point;

1) The AIR (or Mutual information) in DtiStudio is for "intra-subject
intra-DTI" image registration. DTI data consists of b0 images and
diffusion-weighted images; typically there are tens of images, which need to
be all co-registered before tensor calculation.

2) After tensor calculation, b0 and all tensor-derived maps (FA, color,
eigenvalues) are all naturally co-registered each other and no further
registration by AIR is not needed.

3) For intra-subject inter-contrast (e.g. T2 and b0/DTI) or inter-subject
registration, you need to use DiffeoMap. This also include intra-subject but
scanned at different time points.

4) In general, cross-contrast registration (e.g. b0 vs T1) is difficult.

Now, going back to your question, I'm not sure if you want intra-subject
(+intra-DTI) or inter-data registration, but I guess the following steps are
what you want;

> Get two b0s from subject A and B and load them into DiffeoMap. The first
image you open (in this case A) will the the template.
> Do image registration by, for example, AIR, save the transformation
matrix.
> Load FA, trace, and other DTI-derived images of B and apply the
transformation matrix.

Hope this will help.

Susumu

On Sat, Aug 7, 2010 at 12:53 PM, Jan Tillema <Jan.Tillema at cchmc.org> wrote:

>  Dr. Mori,
>
> Thank you very much for your help on my last questions.  In response to
> your answer on my questions from Jul 28 (regarding DTI data before/after
> intervention) - see below for details - I have a follow up question:
>
> I have only used DTIstudio and ROIEditor, and am not too comfortable with
> Diffeostudio yet. Since you mentioned to try linear transformation I tried
> the following using AIR in DTIstudio.
> - I have all my processed data saved in analyze format - so I loaded these
> in DTIstudio.
> - using rigid body transformation with AIR I get really nice results for
> co-registration of B0 images before & after treatment, but when I use the FA
> maps and individual val0,1&2 & color maps this (not fully surprising) don't
> always correlate well.
> - I saved the AirMatrix.txt file from the B0 transformation
> My questions:
> --- How can I transform the other images (FA, val0, val1, val2, color map)
> using this Matrix???
> --- Can this be done using DTIstudio or will that have to be done in
> Diffeomap
> --- Is this an acceptable way to do it as long as the B0 images correspond
> (which they visually do nicely) and is there an easier way to do this using
> Diffeomap?
>
> Thanks
>
> JMT
>
>
> On Wed, Jul 28, 2010 at 4:01 PM, Jan Tillema <Jan.Tillema at cchmc.org<http://lists.mristudio.org/mailman/listinfo/mristudio-users>>
> wrote:
>
> >*  I have a similar question.
> *>* We have dataset of subjects before/after intervention, we have 15 dir
> DTI
> *>* and 3D T1 data (GE) with same parameters both times, but orientation
> not
> *>* exactly the same (clinical protocol). The brains are not normal at
> baseline
> *>* with enlarged ventricles that may have changed minimally (due to
> treatment,
> *>* e.g. smaller size). Normalization is not a possibility d/t
> abnormalities on
> *>* brain to begin with, we just want to compare before/after. We are
> *>* investigating the effect on white matter and would like to get best
> approach *>* to compare basic measurement before/after. We have manual
> (blinded) ROI
> *>* showing differences before/after, but want to make sure we are in the
> exact
> *>* same ROI. To co-register seems the best way, but tricky as the
> structure of
> *>* the brain is not exactly the same. Any suggestions?
> *>*
> *>* 1) would it be best to co-register DTI to T1 at both time points and
> then
> *>* to co-register T1 in time point A to B followed by change of DTI with
> same
> *>* matrix? If so, I assume this would have to be done with DiffeoMap,
> what
> *>* would be the steps to do so?
> *>*
> *
> Unless there is a reason that you want T1-DTI be registered (e.g. ROI drawn
> in T1, FA measured in DTI), I think you can directly register DTI to DTI.
> Yes, DiffeoMap should be able to do it.
>
>
> >* 2) is co-registration to "dangerous" for bias as there is the
> possibility
> *>* that the brain is not exactly the same before and after (ventricle
> size
> *>* change)
> *>*
> *
> First you have to decide if you want only linear transformation adjusting
> the overall head positions or do non-linear to remove the tissue
> deformation
> due to the surgery. I suspect you want the former (I think the latter is
> difficult).
>
> Linear transformation is mostly driven by brain boundary. So, you can
> assume
> that as long as the tissue deformation is mostly inside the brain and the
> brain boundary shape remains the same, the linear transformation should be
> able to match the two brains. However, we have seen not-so-perfect linear
> registration even between two images from the same person. Reason could be;
> the initial alignment was way off, there is an intense sinus signal in one
> of them, etc. In the end, it is your subjective judgment if the linear
> registration is satisfactory. If there is a good quantitative way to judge
> the alignment, we would have used such a metric to drive the linear
> registration.
>
> In your case, you may want to try the landmark function of DiffeoMap. You
> need at least 3 point landmarks to define the corresponding structures
> between the two images. Unfortunately there are not many point landmarks
> inside the brain. The exceptions are AC and PC. The third point could be
> some easy-to-define structures in the brainstem at the mid-sagittal level
> such as the junction of the pons and midbrain. If you can clearly find
> these
> 3 points, place these landmarks in both images and use rigid alignment.
>
> Let us know if this approach works.
>
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