| % geticvariance() - compute variance of independent component activations | |
| % during saccade and fixation intervals | |
| % | |
| % Usage: | |
| % >> [varsac,varfix] = geticvariance(EEG,sacstring,fixstring,tolerance) | |
| % | |
| % Inputs: | |
| % sacstring - [string] name of saccade event in EEG.event.type. | |
| % this is usually 'saccade', but may differ (e.g. 'L_saccade') | |
| % if saccades were imported from Eyelink raw data | |
| % fixstring - [string] name of fixation event in EEG.event.type. | |
| % this is usually 'fixation', but may differ if fixations were | |
| % imported from Eyelink raw data | |
| % tolerance - [vector with two integers] defines the tolerance around | |
| % saccade onset and saccade offset (in samples). | |
| % IC variance during saccade intervals will be computed from | |
| % saccade-onset minus tolerance(1) samples until saccade-offset | |
| % plus tolerance(2) samples. Conversely, tolerances are | |
| % subtracted from the fixation intervals. Two positive | |
| % integers are expected. | |
| % | |
| % Outputs: | |
| % varsac - [vector of length ncomp] mean variance during saccade intervals | |
| % | |
| % varfix - [vector of length ncomp] mean variance during fixation intervals | |
| % | |
| % output(:,1): mean IC variance during saccade intervals | |
| % output(:,2): mean IC variance during fixation intervals | |
| % output(:,3): ratio sac/fix variance, i.e.: output(:,1)./output(:,2) | |
| % Ratios above 1 indicate that the component is more active | |
| % during saccades than during fixations and thus likely | |
| % to reflect corneoretinal or myogenic ocular artifact | |
| % | |
| % See also: eyetrackerica, pop_eyetrackerica, geticvariance | |
| % | |
| % Author: od | |
| % Copyright (C) 2009-2013 Olaf Dimigen & Ulrich Reinacher, HU Berlin | |
| % olaf.dimigen@hu-berlin.de / ulrich.reinacher.1@hu-berlin.de | |
| % This program is free software; you can redistribute it and/or modify | |
| % it under the terms of the GNU General Public License as published by | |
| % the Free Software Foundation; either version 3 of the License, or | |
| % (at your option) any later version. | |
| % | |
| % This program is distributed in the hope that it will be useful, | |
| % but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| % GNU General Public License for more details. | |
| % | |
| % You should have received a copy of the GNU General Public License | |
| % along with this program; if not, write to the Free Software | |
| % Foundation, 51 Franklin Street, Boston, MA 02110-1301, USA | |
| function [varsac,varfix] = geticvariance(EEG,sacstring,fixstring,tolerance) | |
| if length(tolerance) ~= 2 | |
| error('%s(): tolerance needs to be a vector with two entries.') | |
| end | |
| tolerance = abs(tolerance); | |
| %% get activation time courses of ICs | |
| if isempty(EEG.icaact) | |
| icaact = eeg_getica(EEG); | |
| else | |
| icaact = EEG.icaact; | |
| end | |
| if size(EEG.data,3) == 1 % data is continouos | |
| continuous = true; | |
| else | |
| icaact = icaact(:,:); % convert to 2D | |
| continuous = false; | |
| end | |
| epochlength = size(EEG.data,2); | |
| %% get latencies (onset sample) of saccade & fixation events | |
| ix_sac = find(ismember({EEG.event.type},sacstring)); | |
| ix_fix = find(ismember({EEG.event.type},fixstring)); | |
| if ~isempty(ix_sac) && ~isempty(ix_fix) | |
| % preallocate | |
| varsac = NaN(size(icaact,1),length(ix_sac)); | |
| varfix = NaN(size(icaact,1),length(ix_fix)); | |
| % latencies and durations of EMs (in samples) | |
| saclat = [EEG.event(ix_sac).latency]; | |
| sacdur = [EEG.event(ix_sac).duration]; | |
| fixlat = [EEG.event(ix_fix).latency]; | |
| fixdur = [EEG.event(ix_fix).duration]; | |
| % go tru saccades | |
| fprintf('\n-- Calculating IC variance during %i saccades...',length(ix_sac)); | |
| for ns = 1:length(ix_sac) | |
| % define samples belonging to saccade (with tolerance) | |
| lowr = saclat(ns) - tolerance(1); | |
| uppr = saclat(ns) + round(sacdur(ns))-1 + tolerance(2); | |
| if lowr <= 0, lowr = 1; end | |
| if uppr > size(icaact,2), uppr = size(icaact,2); end | |
| if ~continuous | |
| same_epoch = false; | |
| % epoched data: make sure data is from same epoch | |
| epoch_lowr = floor((lowr-1)/epochlength)+1; % epoch @ start of window | |
| epoch_uppr = floor((uppr-1)/epochlength)+1; % epoch @ end of window | |
| if epoch_lowr == epoch_uppr | |
| same_epoch = true; | |
| end | |
| end | |
| if continuous || same_epoch | |
| % get icaact variance within this saccade | |
| varsac(:,ns) = var(icaact(:,lowr:uppr),0,2); | |
| end | |
| end | |
| fprintf(' computed for %i of %i saccade intervals', sum(~isnan(varsac(1,:))),ns); | |
| % go tru fixations | |
| fprintf('\n-- Calculating IC variance during %i fixations...',length(ix_fix)); | |
| for nf = 1:length(ix_fix) | |
| % define samples belonging to fixation (with tolerance) | |
| lowr = fixlat(nf) + tolerance(2); | |
| uppr = fixlat(nf) + round(fixdur(nf))-1 - tolerance(1); | |
| % at least 2 samples left of fixation interval to compute variance? | |
| if lowr < uppr-1 | |
| if ~continuous | |
| % data is epoched: make sure data is from same epoch | |
| same_epoch = false; | |
| epoch_lowr = floor((lowr-1)/epochlength)+1; % epoch @ start of window | |
| epoch_uppr = floor((uppr-1)/epochlength)+1; % epoch @ end of window | |
| if epoch_lowr == epoch_uppr | |
| same_epoch = true; | |
| end | |
| end | |
| if continuous || same_epoch | |
| % get icaact variance within this saccade | |
| varfix(:,nf) = var(icaact(:,lowr:uppr),0,2); | |
| end | |
| else | |
| % catch extreme scenario: fixation duration is only 1 sample or | |
| % the tolerance around saccade is set so high that the | |
| % remaining fixation interval is not even 2 samples long | |
| %fprintf('\nWarning: Remaining samples to compute fixation variance was less than 2 samples long. Skipped.') | |
| end | |
| end | |
| fprintf(' computed for %i of %i fixation intervals', sum(~isnan(varfix(1,:))),nf); | |
| if sum(~isnan(varsac(1,:))) ~= ns | |
| fprintf('\nNote: Variance was not computed for all saccade intervals, because intervals exceeded the epoch boundaries.'); | |
| end | |
| if sum(~isnan(varfix(1,:))) ~= nf | |
| fprintf('\nNote: Variance was not computed for all fixation intervals, because intervals exceeded the epoch boundaries.\n'); | |
| end | |
| % get mean sac and fix variances and the variance ratio (sac/fix) | |
| varsac = nanmean(varsac,2); | |
| varfix = nanmean(varfix,2); | |
| else | |
| % error message: no saccade or fixation events of this name found in EEG.event.type | |
| if isempty(ix_sac) | |
| if isempty(ix_fix) | |
| error('%s(): There are neither saccade events nor fixation events called \"%s\" or \"%s\" in EEG.event.type!', mfilename,sacstring,fixstring) | |
| else | |
| error('%s(): Fixation events found, but found no saccade events called \"%s\" in EEG.event.type!', mfilename, sacstring) | |
| end | |
| else | |
| error('%s(): Saccade events found, but found no fixation events called \"%s\" in EEG.event.type!', mfilename, fixstring) | |
| end | |
| end |