If a base anatomy has a Talairach transformation assigned to it, mrTools will display Talairach coordinates when that base is being viewed. In addition, any ROIs defined on a base with Talairach can be aligned to ROIs from any other brain, on the basis of the Talairach values. mrTools does all of this automatically, and gives specific warnings and instructions so that you are aware if this is happening.
The way we've implemented the use of registration to the Talairach coordinate system is by keeping track of a single transform. We don't currently support anything other than a single transformation of the whole brain. Once a transform is defined for a given brain, (see below) it can be saved to the base volume for that brain and then it will be inherited by everything aligned to or defined on that base volume. In this way, scans and ROIs from different subjects can be aligned with one another by transforming to Talairach space instead of magnet space. This happens behind the scenes, so that scan2scan and base2base and roi2roi are all computed using the Talairach transform if it's available.
To assign a Talairach transformation to a volume anatomy, you will need to load it in mrAlign, and then follow these steps:
Load volume anatomy in mrAlign
In the mrAlign menu bar, pull down the 'Talairach' tab and select 'Set Talairach Transform'
This will open four windows: three volume views (sagittal, coronal, axial), and a point-setting command center. For detailed instructions on how to use this interface, go to How to Set Talairach Coordinates
Using the 3 viewing windows, determine the location of the anchoring points (e.g., AC, PC, SAC, etc). I find this website
helpful for determining the correct location of AC and PC.
For each anchor point, when you are happy with your choice, pull down the 'setPoint' menu and select the point you have assigned.
For choosing AAC and PPC, and LAC and RAC, it is useful to use the displayPlane and straighten buttons so that you are viewing the volume in the corrected AC/PC plane. [NOTE: To start over without saving, hit 'Cancel']
When you're done, hit 'OK.' This automatically saves the rotation matrix that has been calculated based on the anchor points. The rotation matrix is saved in the .mat file that exists for every base anatomy. As the inplane anatomies and functional scans are aligned to this volume, the correct rotation matrix will be inherited at each step.
If you need to adjust your Talairach points at a later date, follow steps 1-7. Then, under the Talairach file menu, choose 'Export Talairach.' This will allow you to correct the transformation for any files that have been created based on the volume you have changed.
How the chosen points are used by mrLoadRet
We keep everything in the base structure, and we don't change the NIFTI headers, e.g., we do not re-set sform code to 3, we do not actually rotate the volume, and we do not change the s-form. Rather, we leave the sform code as 1, and save talXform to the base structure to be used for viewing or aligning.
See here for details of how talXform is computed, from points chosen by the user.
Volume Anatomy Rotations (Order of Dimensions)
If you think something might be going wrong because the voxels in your volume anatomy aren't in the right order, here are some instructions to help you figure it out.