# Plotting a downsampled source space together with a .label file **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [July 31, 2013, 10:01pm UTC](https://mne.discourse.group/t/plotting-a-downsampled-source-space-together-with-a-label-file/601 "2013-07-31T22:01:18Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [July 31, 2013, 10:01pm UTC](https://mne.discourse.group/t/plotting-a-downsampled-source-space-together-with-a-label-file/601/1 "2013-07-31T22:01:18Z")
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](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](http://i.imgur.com/IGlKB9T.png) and [http://i.imgur.com/CUj6cF7.png](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 ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [July 31, 2013, 10:26pm UTC](https://mne.discourse.group/t/plotting-a-downsampled-source-space-together-with-a-label-file/601/2 "2013-07-31T22:26:12Z")
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 ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [August 2, 2013, 2:30pm UTC](https://mne.discourse.group/t/plotting-a-downsampled-source-space-together-with-a-label-file/601/3 "2013-08-02T14:30:04Z")
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](http://files.nyu.edu/spa268/public)