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Bug 868 - ft_neighbourselection miss sensors after ft_rejectcomponent
| Status | CLOSED FIXED |
| Reported | 2011-08-15 17:43:00 +0200 |
| Modified | 2011-10-05 15:07:28 +0200 |
| Product: | FieldTrip |
| Component: | core |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Linux |
| Importance: | P1 normal |
| Assigned to: | Jan-Mathijs Schoffelen |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Diego Lozano Soldevilla - 2011-08-15 17:43:30 +0200
Created attachment 114 gradiometers before and after IC rejection Missing sensors calculating ft_neighbourselection after reject ICs. I attach gradometers before (grad_ori) and after (grad_afterICrej) IC rejection. With the followed pipeline, the lost channel is MLT31 (sensor number 111): cfg = []; cfg.dataset = 'VOGTHAdielozS06.ds'; cfg.trialdef.eventtype = 'frontpanel trigger'; cfg.trialdef.eventvalue = 4; cfg.trialdef.prestim = 1.5; % in seconds cfg.trialdef.poststim = 3.7; % in seconds cfg.trialdef.epochmoving = 'multnormal'; cfg.trialdef.taskfile = [gendir dgendir(subj,1).name '/task_behavior/' dgendir(subj,1).name '_behav_EXP_results.mat'];%path to load beahvior info; cfg.trialdef.buttonresp = [97 98]; cfg.trialfun = 'trialselec_rt'; cfg = ft_definetrial(cfg); %MEG preprocessing cfg.channel = {'MEG'}; cfg.lpfilter = 'yes'; cfg.lpfreq = 210; cfg.keeptrials = 'no'; cfg.demean = 'no'; cfg.detrend = 'yes'; cfg.continuous = 'yes'; cfg.trl = cfg.trl(1:3,:); meg = ft_preprocessing(cfg); load('/home/electromag/dieloz/MEG/VOGTHA_3016028.02/participants/VOGTHAdielozS06/raw_data/VOGTHAdielozS06_delay_rt_meg_sum_icaW.mat')%this is my IC inverse weights' matrix saved as comp variable %demixing MEG sensors cfg = []; cfg.topo = comp.topo; cfg.topolabel = comp.topolabel; clear comp; meg = ft_componentanalysis(cfg, meg); component=[3 6 16 24 30]; %rejecting previous selected ICs cfg = []; cfg.component = [component]; meg = ft_rejectcomponent(cfg, meg); cfg.feedback = 'yes'; %cfg.method = 'distance'; %cfg.neighbourdist = 5; cfg.method = 'triangulation'; %cfg.method = 'template'; cfg.neighbours = ft_neighbourselection(cfg, meg);
Jan-Mathijs Schoffelen - 2011-08-17 10:05:49 +0200
I made a fix. @Diego: can you test it and let me know whether it works?
Diego Lozano Soldevilla - 2011-08-17 13:55:42 +0200
(In reply to comment #1) > I made a fix. @Diego: can you test it and let me know whether it works? I run the code that I sent you but when I'm in the ft_neighbourselection step, Matlab is hanging (In ducth "vast lopen"?). When I press crtl+c this is what I get: Using the gradiometer configuration from the dataset. undoing the invcomp balancing Warning: the linear projection for the montage is not full-rank, the resulting data will have reduced dimensionality > In ft_apply_montage at 76 In fieldtrip/private/undobalancing at 30 In fieldtrip/private/channelposition at 31 In ft_neighbourselection at 110 undoing the comp balancing undoing the G3BR balancing ??? Operation terminated by user during ==> channelposition at 77 In ==> ft_neighbourselection at 110 [sens.pnt, sens.label] = channelposition(sens); Any ideas??
Jan-Mathijs Schoffelen - 2011-08-17 19:55:34 +0200
Hi Diego, We decided to solve this in a different way. This will need some substantial changes to the code and will take a while. For now I'd advice you to either: -copy a grad-structure from a data-structure before you start applying the componentanalysis and rejectcomponent, or -use the template method for the neighbourhoodselection.