[Mne_analysis] Plotting a downsampled source space together with a .label file

[Stephen Politzer-Ahles]

Thanks, that solved it! It was indeed the second issue; plotting my label
by using the vertex numbers instead of the positions from the label file
worked perfectly.

Best,
Steve

Stephen Politzer-Ahles
New York University, Abu Dhabi
Psychology Department
http://files.nyu.edu/spa268/public


On Wed, Jul 31, 2013 at 6:26 PM, Eric Larson <larson.eric.d at gmail.com>wrote:

> Hey Steve,
>
> Offhand I see a couple possibilities. If you're referencing by vertex
> numbers, you might be hitting off-by-one errors somewhere, since MATLAB
> uses 1-based indexing, and surfaces / vertices are 0-index (C) based. If
> you upload the source space file and label file somewhere, someone (maybe
> me) might be able to track down what's going on. For what it's worth, if
> you have a working mne-python install, it uses 0-based indexing, and has
> useful functions for plotting brains with labels and the like. By OBO
> errors in my experience make usually result in worse errors, so that's
> probably not it.
>
> If you're getting the positions directly from the label file, one thing
> you might want to check is the positions you get if you take the vertices
> referenced in the label file and use those to get positions in the source
> space. (In this case, be careful about the indexing...) Label files contain
> position values (what I have a feeling you're using to make the plots), but
> they also contain vertex numbers that those are meant to correspond to in
> source space.  You might be hitting a problem where the label locations are
> pulled from one surface (e.g., pial), while the source space is defined
> over another (e.g., orig). I usually do my source-space manipulations using
> vertex numbers (instead of positions) to avoid this issue completely, as it
> treats all surfaces (e.g., pial, orig, sphere) equally.
>
> Eric
>
>
>
> On Wed, Jul 31, 2013 at 3:01 PM, Stephen Politzer-Ahles <
> politzerahless at gmail.com> wrote:
>
>> Hello,
>>
>> I am trying to plot a mesh of points from a sourcespace (e.g.,
>> $SUBJECTS_DIR/$SUBJECT/bem/$SUBJECT-ico-4-src.fif) together with the points
>> in the label file. (the reason is because we made some custom labels using
>> a script, and they turned out looking patchy--see
>> http://imgur.com/bUAuaJH--so I want to check whether these labels really
>> cover the whole regions they're supposed to, or whether there are
>> sources/vertices that should be in those labels but aren't.) However, when
>> I do this, the locations of the vertices from the label file don't quite
>> line up with vertices from the source space (see
>> http://i.imgur.com/IGlKB9T.png and http://i.imgur.com/CUj6cF7.png for
>> comparisons; the green vertices from the label file are in more or less the
>> right place [what's plotted here is Brodmann area 46], but don't quite line
>> up with the black vertices from the source space), which I was surprised
>> by, since I thought the locations of vertices in a label file came directly
>> from the source space. What I was doing was reading the -ico-4-src.fif file
>> into MATLAB using the FieldTrip toolbox, and reading a label file in
>> directly, and then plotting them together.
>>
>> So I am just wondering if there is a different file I should be using to
>> plot the locations of all the vertices in my sourcespace that labels could
>> have come from? Otherwise I guess it's a problem with how we created the
>> labels.
>>
>> Thank you,
>> Steve Politzer-Ahles
>>
>> ----
>> Stephen Politzer-Ahles
>> New York University, Abu Dhabi
>> Psychology Department
>> http://files.nyu.edu/spa268/public
>>
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