If you do a FMR - VMR coregistration in BrainVoyager, it is quite hard to interpret the resulting Initial and Fine Tuning alignment matrices. There are a lot of transformations that are not stored in the initial alignment matrix, but can be deduced from header information like the resolution and dimensions of the data, and also the slice scanning order of the FMR.
With the Matlab code provided here, you will be able to replicate the aligment in Matlab and also understand how to go from a FMR to a VMR coordinate, or the other way around. It will show you in a understandable way how the final transformation matrix is created.
FMR displayed inside VMR VMR displayed in FMR space
Besides giving insight into the world of BrainVoyager transformation matrices, this matlab code also provides you with a basis that you can extend to e.g.:
- Extract the anatomical information belonging to a certain functional voxel
- Go from the coordinate in one FMR to the corresponding coordinate in a second FMR by using the VMR as step in between
- Project FMR activation maps back into the VMR, allowing you to do analysis on uninterpolated functional data
Download the Matlab code here (and make sure you have installed Neuroelf before you use it)