In the rare case that your anatomical data is not of same dimensions in-plane --i.e. x:256 y:192, z:192-- which can give problems for the initial alignment of the coregistration, you can correct this as follows:
- Create VMR project
- Click "Cancel" at the "Contrast/Brightness" window
- Next a window pops up asking for transformation to saggital format. Click "No".
- Go to "VMR Properties-->Options" dialog
- At the "Center data in new dimensions.." field, check whether it displays New xdim 256, New ydim 256, New zdim 256 and click "Frame". Save the VMR.
- Go to "3D Volume tools-->Spatial Transformations". Click the "To Sag" button, and click yes in the pop-up window.
- Check the result. This should be in the BV standard representation.