MEDx Frequently Asked Questions - Registration

Q: How do I Render Statistical Results Derived from Coronal Partial Volume EPI with Anatomical Data in Talairach Space?

In most functional imaging studies the resolution of the functional image data is much less than can be obtained with standard structural MRI imaging. Further, statistical analysis of the functional data is typically performed on the functional data in its original space to reduce the memory requirements. To overlay statistical results on the anatomical image it is necessary to register the statistical data with the anatomical data.

Since the statistical data does not contain sufficient anatomical information, registering these results directly with the anatomical data will result in a very poor registration. Instead, we use a method known as Shadow Transformation. A high resolution structural image is acquired as well as a structural image which is co-planer to the coronal partial volume EPI images. The co-planer acquisition has the same number of slices as the EPI images, however the in-plane resolution is higher. First, this co-planer structural image is registered to the high resolution structural image. The resulting transformation can then be saved. The statistical image derived from the EPI images is then resampled to have the same in-plane resolution as the co-planer structural image. The transformation which was saved earlier is then applied (Shadow transformed) to the resampled statistical image. This statistical image will now be in the same space as the high resolution structural MRI. We now place the high resolution structural MRI into Talairach space, save this transformation and apply it to the registered statistical image. This statistical image will now be in Talairach space.

The steps for doing this in MEDx are as follows:

1. Use the AIR dialog box to register the co-planer structural image to the high resolution structural image. The general AIR dialog box can be found under the Registration menu in the toolbox. Since, these two images are from the same subject you should use the Linear Algorithm and the "6 parameter Rigid Body" model for thisregistration. This is an intramodality registration.
   

2. While viewing the result of the registration, choose "Save..." from the "Shadow Transform" menu which is under the Transformation menu in the toolbox. This will save the transform in a file. Simply enter a filename whereyou want the transformation saved.
   

3. Go to the statistical image produced from your functional image analysis. Use the Resample dialog box found under Transformation in the toolbox to set the in-plane resolution of the statistical image to be the same as the co-planer structural image. Typically, it is desired to use Nearest Neighbor interpolation as you are scaling in x and y by a factor of 2 or 4.

4. While viewing the resulting resampled statistical image, choose "Apply..." from the "Shadow Transform" menu. Now, select the file that you saved the transformation in and for the Transform type choose "MotionCorrectionReslice". The application of this transformation will place your statistical image into the same space as your high resolution structural image.

5. Go to the high resolution structural image. Use the Talairach Registration option found under the Registration menu in the toolbox to place this image into Talairach space. Use the Piece-wise Linear option and Trilinear interpolation.

6. Save this transformation to a file as in step (2).

7. Go to the registered statistical image and apply the saved transformation from step (6). This time use the "IntoTalairachSpace" option in the "Apply" transformation dialog box. The application of this transformation will place your statistical image in Talairach space.

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