Re-apply Transformations: Minimize Quality Loss

The steps to transform the data into Talairach space are described elsewhere (Getting Started Guide, step 11). This guide is usefull for preserving quality in the data while going to talairach space. It was originally written as part of a segmentation document and in that way it can be seen as a follow up on the Inhomogeneity Correction and as preparation for the Automatic Segmentation for which we need the Talairach space and optimal data quality.

One may decide to perform the two steps (AC-PC transformation and Talairach warping) first sequentially and to later redo all the transformation in one step (reapplication of transformations) to save quality in the final result.

To save time first, we can perform the single steps in (fast) Trilinear mode, and use the slower, more accurate Sinc mode later in the reapplication.

ACPC transformation


Talairach warping

To be able to “re-apply” transformations performed with the anatomical data, we have to open the final VMR result (CG_MPR_ic_TAL.vmr), and open the VMR properties.

Re-application of spatial transformations

We save the new file as CG_MPR_ic_TAL2.vmr to be able to compare it with the original dataset. To do this, we use the “Load Secondary VMR” option in the File menu.


To overlay the two projects, we choose a zoomed-in view of the axial slice. We can do this either by “CTRL + right-clicking” into the axial slice or by clicking “CTRL + T”.

Switching back and forth using the F8 button is quite helpful in visualising the difference.