I'm trying to view dSPM data in mne_analyze, and found that vertex #s in main windows don't match; at the very bottom, entering vertex # "8912" in the message area brings up "Amplitude at vertex 9865" in source waveform window. If I click on the inflated surface, vertex #s are different in "vert: 8931 value (dSPM): -0.62" portion of the message area, as well as these areas mentioned above.
I'm not sure whether there is a transformation between these 3 display areas, or something went wrong with surface inflation or mne_setup_mri process. If so, could someone suggest ways to figure out at which stage data and surface did not align?
It is difficult to tell from the information you provided, but I
suspect this is a harmless consequence of your forward model settings
and the zoom of your display. I assume that you have used some
downsampling to generate your forward model (either --ico or --grid).
This downsampling means that there isn't a vertex in your forward
model for every point in the inflated/white surface. Because of this
when, you click on a vertex on the inflated surface, MNE will
interpolate this to the nearest vertex in your downsampled forward
model. This is why the 'Amplitude at vertex ...' can conflict with
the number you enter. Furthermore, the surface has hundreds of
thousands of points the likely reason that when you clicked on the
surface a different value came up was that you were actually clicking
on a slightly different vertex.
The easiest way to test this is to zoom in very close so you can see
all the lines from the vertex in question (there should be 5-7 lines
coming from the point in the center these show the nearest points to
this point).
In Labels menu select clear marked vertices.
type in the vertex number that you previously saw as 'vert: ... value
(dSPM): ...'
Now click on the point where all those lines intersect: The value
should not have changed.