Performing manual alignment for functional to anatomical images
Step 1: preparation
First, open the anatomical image (*.vmr). Open the 3D Volume Tools (via 'Volumes' > 3D Volume Tools or via the blue cube on the sidebar). Navigate to the 'Coregistration' tab and click the 'Align FMR...' button. Select the functional image (*.fmr) that should be aligned to the anatomical image (*.vmr). This start situation is shown in the figure below.
Step 2: determination of the transformation parameters
Change the Translation, Rotation and/or Scaling parameters. In the current example the x-axis of the image is rotated by 90 degrees, the y-axis by 180 degrees and the z-axis by 90 degrees. The effective transformation is immediately shown in the lower window.
Step 3: apply or save the transformation
In this step, the transformation can be saved to a transformation file (*.trf) or applied immediately.
To apply the transformation, go to the Fine-Tune Alignment tab of the FMR-VMR Coregistration dialog (via the 'Align...' button). To apply the transformation, select the option 'Manual alignment - use current translation and rotation values' and click 'Run FA' (see figure below).
To save the transformation in order to apply it later, go to the 'Spatial Transf' tab of the 3D Volume Tools and click the 'Save .TRF...' button. The transformation is now saved in a 4 x 4 transformation matrix in a BrainVoyager QX transformation file (*.trf) and can be used for creation of a volume time course file (*.vtc) (in the initial alignment or fine alignment field).
Coregistration of CT and MR images via manual alignment
Import
Import the CT and MR image via 'File' > 'Create new project'. In case of Analyze 7.5 images, use file type 'ANALYZE'. BrainVoyager will ask whether the file should be isovoxelated, i.e. transform the voxel resolution to 1 x 1 x 1 mm. After this has been applied, go to the 'Spatial Transf' tab on the 3D Volume Tools (via 'Volumes > 3D Volume Tools or the blue cube icon on the toolbar). Use the 'To SAG...' button and manipulate the views so that the image is in sagittal orientation. Now, the CT and MR image have the same orientation and same resolution. This means that the transformation is only rigid body; for rigid body transformation we only need to find 6 parameters: translation in x/y/z directions and rotations about the x/y/z axes (see Appendix A for possible search spaces). First open the source image that should be transformed. To start the registration, click 'Select VMR...' on the 'Coregistration' tab of the 3D Volume Tools. When the CT image should be warped to the MR image, then select the MR image now.
Determine parameters for image registration
Determine the rotation and translation parameters to transform one image to the other via the 'Translation' and 'Rotation' boxes on the 'Coregistration' tab of the 3D volume tools (registration via intensity based alignment is less appropriate for the alignment of CT and MR since the intensities of the tissues are different). Manipulate the rotation and translation parameters until the images are overlapping.
Save the transformation in a text file (*.trf) via the 'Save TRF...' button on the Spatial Transf tab. This results in a transformation file, containing the transformation matrix (see figure below) that sends each voxel in one image space to space of the other image.
Close all windows.
Apply the transformation
Open the image that should be transformed and select the transformation file (*.trf) via the 'Load TRF...' button on the Spatial Transf tab. Apply the transformation by clicking the button 'Transform VMR...' on the Spatial Transf tab. This will open the Spatial Transformation of VMR dialog. Select an interpolation degree (Trilinear and Nearest neighbour are fast, Sinc and Cubic spline are precise) and click 'OK' to transform the image.
The transformed image will open automatically. Load the target MR image via File > Secondary VMR or via the Select VMR... button of the 'Spatial Transf tab'. Select a blend display option to check visually whether the alignment is correct. Once the CT and MR are registered to each other, the transformation to Talairach space needs only to be performed for one data set, because the resulting transformation files (*.trf and *.tal) can also be used for the other data set since they have the same position.
For more information about the registration of functional to anatomical images, Step 10 of the BrainVoyager Getting Started Guide can be consulted. Information about the currently available image transformation methods in BrainVoyager can be obtained via the chapters 'Coregistration of Functional and Anatomical Datasets' (https://download.brainvoyager.com/bv/doc/UsersGuide/Coregistration/CoregistrationOfFunctionalAndAnatomicalDataSets.html) and 'Transformation to Normalized Space' (https://download.brainvoyager.com/bv/doc/UsersGuide/BrainNormalization/BrainNormalization.html) of the BrainVoyager User's Guide. For questions, please contact the BrainVoyager support desk via support at brainvoyager.com.