BrainVoyager v23.0

Initial Alignment (IA) Step

The intial alignment step of functional (FMR) and 3D anatomical data (VMR) coregistration can be performed in three different ways:

Mathematical header-based alignment in case that appropriate header information is available
Corresponding points alignment, if the two data sets are from different sessions or when no header information is available
Sagittal reorientation of the functional data. This is the minimal step necessary for a subsequent fine-tuning alignment.

In case of coregistration problems, it might be advisable to run the initial alignment without the subsequent fine-tuning step. This can be achieved by clicking the Run IA button instead of the GO button. If the initial alignment step has been performed, you can re-enter the FMR-VMR Coregistration dialog to start the fine-tuning alignment step. The Run IA button will now be disabled and in the Initial Alignment tab, the option Initial alignment already performed will be selected. This ensures that if the GO button is pressed, only the initial alignment is not repeated and only the fine-tuning adjustment is launched. This can be also achieved, of course, by pressing the Run FA button. You can also inspect the spatial transformation matrix representing the result of the initial alignment by clicking the TRF matrix button in the Initial Alignment tab (see snapshot below).

Sagittal reorientation of the functional data

This method is recommended only if no header information is available and if the two data sets are not misaligned by large displacements, i.e. if the angles during scanning were similar or identical for the functional and anatomical data. In this method only a reorientation of the functional volume into BrainVoyager's standard space is applied by using the To SAG button in the Source Options tab of the FMR-VMR Coregistration dialog. Sagittal reorientation can also be used as the first step of the corresponding points alignment. The details on how to apply the sagittal reorientation are, thus, desccribed in the section "Preparation of the functional volume" in the topic on corresponding points alignment. Sagittal reorientation only performs 90 degree rotations to reorient the functional volume. While the achieved result might be good enough to run the iterative multi-scale fine-tuning alignment step successfully, it is recommended to use the corresponding points alignment to get a better initial FMR-VMR coregistration followed by the fine-tuning alignment step.