# vertex # mismatch in mne\_analyze

**URL:** <https://mne.discourse.group/t/vertex-mismatch-in-mne-analyze/219>\
**Category:** Mailing List Archive (read-only)\
**Tags:** list-archive\
**Created:** [April 15, 2010, 12:53am UTC](https://mne.discourse.group/t/vertex-mismatch-in-mne-analyze/219 "2010-04-15T00:53:00Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [April 15, 2010, 12:53am UTC](https://mne.discourse.group/t/vertex-mismatch-in-mne-analyze/219/1 "2010-04-15T00:53:00Z")

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Hi,

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?

Thanks in advance, Akiko

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**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [April 15, 2010, 8:10am UTC](https://mne.discourse.group/t/vertex-mismatch-in-mne-analyze/219/2 "2010-04-15T08:10:18Z")

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Hi Akiko,

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.

D