Dear Gianna,
you may want to check the headers of Va and Vb in order to see whether one of the images has a different spatial orientation than the other. spm_read_vols gives you the raw data matrix for each image. If one of the images is stored left-handed and the other one stored right-handed the same pixel coordinates in Va and Vb will map to different world coordinates.
If you can formulate your intersection expression as a formula for ImCalc, I would suggest you use this tool. This way, you don't need to worry any more about spatial orientation and resolution issues.
Hope this helps,
Volkmar
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