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Keithchanges. Stim measurements and file formats #1

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f8712e5
Modified to handle new behave XML format, and to handle .hdf5 movie f…
kjamison Mar 4, 2015
d774e78
Correct stimulus viewing distance and diameter
kjamison Oct 5, 2015
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30 changes: 19 additions & 11 deletions MATLAB/RetinotopyAnalysis.m
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Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,8 @@ function RetinotopyAnalysis(inputfile)
%%%%% SETUP

% internal constants
viewingdistance = 39; % inches
widthofstim = 15; % inches
viewingdistance = 101.5; % cm
widthofstim = 28.5; % cm
wbcmd = 'wb_command'; % workbench command
tr = 1; % seconds
stimres = 200; % number of pixels along each dimension of the stimulus
Expand Down Expand Up @@ -80,15 +80,23 @@ function RetinotopyAnalysis(inputfile)
% load stimuli
stimulus = {}; % each element is 200 x 200 x 300, single format
for p=1:length(movie_files)
a1 = load(movie_files{p});
stimulus{p} = a1.stim;
[~,~,ext]=fileparts(movie_files{p});
switch lower(ext)
case '.mat'
a1 = load(movie_files{p});
stimulus{p} = a1.stim;
clear a1;
case '.hdf5'
stimulus{p} = hdf5read(movie_files{p},'/stim');
case '.mov'
mobj = VideoReader(movie_files{p});
stim0 = read(mobj);
stimulus{p} = permute(single(stim0(:,:,1,:)),[1 2 4 3]);
clear mobj stim0;
otherwise
error('Unknown movie file type: %s\n',movie_files{p});
end
end
clear a1;
% ALTERNATIVE:
% mobj = VideoReader(movie_files{p});
% stim0 = read(mobj);
% stimulus{p} = permute(single(stim0(:,:,1,:)),[1 2 4 3]);
% clear stim0;

% sanity check
assert(length(stimulus)==5);
Expand All @@ -105,7 +113,7 @@ function RetinotopyAnalysis(inputfile)
behaviors{p} = [];
else
a1 = xml2struct(behavior_files{p}); % relevant fields: expttype (1-5), ttlStamps
behaviors{p} = a1.ret_summary;
behaviors{p} = a1.behav_summary;
end
end
clear a1;
Expand Down
7 changes: 4 additions & 3 deletions RetinotopyAnalysis.sh
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Expand Up @@ -80,7 +80,8 @@ usage() {
echo " : id of subject for the data being processed"
echo ""
echo " --movie-files=<file-list>"
echo " : @ symbol separated list of movie files (QuickTime files) used as stimuli for the retinotopy task"
echo " : @ symbol separated list of movie files used as stimuli for the retinotopy task"
echo " Expects Quicktime .mov files, Matlab .mat files, or .hdf5
echo ""
echo " --image-files=<file-list>"
echo " : @ symbol separated list of minimally preprocessed functional \(fMRI\) image files"
Expand Down Expand Up @@ -124,7 +125,7 @@ usage() {
# Global output variables
# ${userid} - input - user login id
# ${subject} - input - subject id
# ${movie_files} - input - @ symbol separated list of movie files (QuickTime files) used as stimuli for the
# ${movie_files} - input - @ symbol separated list of movie files (mov,mat,or hdf5) used as stimuli for the
# retinotopy task
# ${image_files} - input - @ symbol separated list of minimally preprocessed functional (fMRI) image files
# ${behavior_files} - input - @ symbol separated list of behavior files from which time offsets can be obtained
Expand Down Expand Up @@ -238,7 +239,7 @@ main() {
# Global Variables Set
# ${userid} - input - user login id
# ${subject} - input - subject id
# ${movie_files} - input - @ symbol separated list of movie files (QuickTime files) used as stimuli for the
# ${movie_files} - input - @ symbol separated list of movie files (mov,mat,or hdf5) used as stimuli for the
# retinotopy task
# ${image_files} - input - @ symbol separated list of minimally preprocessed functional (fMRI) image files
# ${behavior_files} - input - @ symbol separated list of behavior files from which time offsets can be obtained
Expand Down