Yes, this is possible. Here are the steps to accomplish this.
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Choose “Three over three” layout and put one volume in the upper row and the other in the lower row
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Create two markups fiducial nodes (in the most recent versions of Slicer, these have been renamed “Point List”)
I called mine “F” and “G”. -
In the Markups module, select the first node (“F” for me), then expand the “Display” section, and then the “Advanced” section within the “Display” section. The top entry is “View:” and the default is “All”, which means that points in this point list will appear on all slice and all 3D views.
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Click the dropdown, and uncheck the bottom row slice views (these are “Red+”, “Green+”, and “Yellow+”). This will mean that points in “F” are not visible in the bottom row views.
- Do the same for the other point list (“G”). First select it on the list of nodes at the top, then click the “View:” dropdown, and this time uncheck “Red”, “Green”, and “Yellow”. This will make “G” points invisible in the top row of slice views.
Following these instructions, both sets would be visible in the 3D view when present; if that is not what you want, then you can hide either or both in the 3D view by unchecking “View1” in the “View:” dropdown list.
If you haven’t already, I would recommend taking a look at the “Fiducial Registration Wizard” module from the “SlicerIGT” extension (installable from the Extension Manager). The “Landmark Registration” module included in core Slicer is supposed to do something similar, but I have always found it very difficult to use and not at all intuitive.