[Mristudio-users] co-registration question.

[Jan Tillema]

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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