Back to the main page.
Bug 3475 - ft_plot_sens wont plot labels of a linear array of electrodes
| Status | CLOSED FIXED |
| Reported | 2019-06-05 02:17:00 +0200 |
| Modified | 2019-08-10 12:43:46 +0200 |
| Product: | FieldTrip |
| Component: | plotting |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Mac OS |
| Importance: | P5 normal |
| Assigned to: | Robert Oostenveld |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Arjen Stolk - 2019-06-05 02:17:21 +0200
PROBLEM SIMULATION: elec.label = {'elec1','elec2','elec3','elec4','elec5'}'; elec.elecpos(:,1) = [1 2 3 4 5]; elec.elecpos(:,2) = [1 1 1 1 1]; elec.elecpos(:,3) = [1 1 1 1 1]; elec.chanpos = elec.elecpos; elec.unit = 'mm'; ft_plot_sens(elec, 'label', 'on') ... results in no labels shown, or as experienced using real data, throws the following error: Error using builtin The data is degenerate in at least one dimension - ND set of points lying in (N+1)D space. Error in qhullmx Error in convhulln (line 64) [k,vv] = qhullmx(x', opt); Error in projecttri (line 57) tri = convhulln(pos); Error in ft_plot_sens (line 298) tri = projecttri(pos); POTENTIAL SOLUTION: reorganize lines 293-313 to be more robust somehow, e.g. skipping the attempt to triangulate? for convenience, the code is: if isempty(ori) && ~isempty(pos) if ~any(isnan(pos(:))) % determine orientations based on surface triangulation tri = projecttri(pos); ori = normals(pos, tri); else % determine orientations by fitting a sphere to the sensors try tmp = pos(~any(isnan(pos), 2),:); % remove rows that contain a nan center = fitsphere(tmp); catch center = [nan nan nan]; end for i=1:size(pos,1) ori(i,:) = pos(i,:) - center; ori(i,:) = ori(i,:)/norm(ori(i,:)); end end end
Arjen Stolk - 2019-06-05 03:05:57 +0200
Note the triangulation approach also won't work for electrode arrays smaller than 3. ft_plot_sens(elec, 'label', 'on'); Error using delaunay At least three input points must be provided to define a triangular mesh.
Arjen Stolk - 2019-06-08 07:15:43 +0200
https://github.com/fieldtrip/fieldtrip/commit/0e5489cd5e6982d7683b560db0fa80b297f4f345#diff-d83112eee816b56d32479d35e56dab63 is the version in which projecttri was introduced
Robert Oostenveld - 2019-06-11 15:17:30 +0200
The most common set of electrodes is for scalp EEG, where the outward displacement from the scalp surface (= the electrode triangulation) works well. Plotting the labels on top of the electrodes is not very good. I propose that a try-catch is added to the code to deal with electrode sets for which a triangulation cannot be determined.
Robert Oostenveld - 2019-06-11 15:20:34 +0200
note that I recently changed the triangulation from convex hull into delaunay https://github.com/fieldtrip/fieldtrip/commit/3335f5c2fd6f96f0bff18a851d0073846e21e744 That results in an open (at the bottom) triangulation instead of a closed one, which means that the label-displacement for the lower line of electrodes is better. The consequence is also that the "degenerate" error does not show up any more. But the labels for the linear array still don't show.
Robert Oostenveld - 2019-06-11 15:48:52 +0200
[bug3475 2159c5c24] FIX #3475 - improve plotting of electrode labels for linear arrays 3 files changed, 111 insertions(+), 20 deletions(-) create mode 100644 test/test_bug3475.m https://github.com/fieldtrip/fieldtrip/pull/1140 Have a look at the test script. Please reopen if you think that more work is needed.
Robert Oostenveld - 2019-06-11 15:49:15 +0200
The specific example now looks fine