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t_glmRun

Illustrates how to run a GLM on a functional data set.

Tested 01/04/2011 - MATLAB r2008a, Fedora 12, Current Repos

Stanford VISTA

Contents

Initialize the key variables and data path:

Data directory (where the mrSession file is located)

dataDir = fullfile(mrvDataRootPath,'functional','vwfaLoc');
parfDir = fullfile(dataDir, 'Stimuli', 'parfiles');

% You must analyze with the matlab directory in the data directory.
curDir = pwd;   % We will put you back where you started at the end
chdir(dataDir);


% There can be several data types - we're using motion compensated dated
dataType = 'MotionComp';

Get data structure: 

vw = initHiddenInplane(); % Foregoes interface - loads data silently

Prepare scans for GLM 

numScans = viewGet(vw, 'numScans');
whichScans = 1:numScans;

% If you're processing your own experiment, you'll need to produce parfiles
% More info @
% http://white.stanford.edu/newIm/index.php/GLM#Create_.par_files_for_each_scan
whichParfs = {'VWFALocalizer1.par' ...
'VWFALocalizer2.par' ...
'VWFALocalizer3.par'};


vw = er_assignParfilesToScans(vw, whichScans, whichParfs); % Assign parfiles to scans
vw = er_groupScans(vw, whichScans, [], dataType); % Group scans together

Set GLM Parameters:

The GLM parameters are stored in a Matlab structure. We call the structure params. The parameters, such as params.timeWindow inform the GLM processing routine about the experiment.

A description of the parameters can be found on the wiki at:

http://white.stanford.edu/newlm/index.php/MrVista_1_conventions#eventAnalysisParams

params.timeWindow               = -8:24;  %
params.bslPeriod                = -8:0;   %
params.peakPeriod               = 4:14;   %
params.framePeriod              = 2;      % TR
params.normBsl                  = 1;
params.onsetDelta               = 0;
params.snrConds                 = 1;
params.glmHRF                   = 2;
params.eventsPerBlock           = 6;
params.ampType                  = 'betas';
params.detrend                  = 1;
params.detrendFrames            = 20;
params.inhomoCorrect            = 1;
params.temporalNormalization    = 0;
params.glmWhiten                = 0;

saveToDataType = 'GLMs'; % Data type the results will be saved to

Run GLM:

Returns view structure and saved-to scan number in new data type

[vw, newScan] = applyGlm(vw, dataType, whichScans, params, saveToDataType);

% newScan indicates the scan # in which results are saved
% vw is a mrVista view structure.  If you just type vw, you will see a lot
% of the fields.  In this case, many of them are empty.  To understand what
% the fields can represent, see the vistalab wiki re: GLMs.

To delete the new GLM run: 

removeScan(vw, newScan, saveToDataType, 1);

END


Published with MATLAB® R2013b

<!--
SOURCE BEGIN

%% t_glmRun % % Illustrates how to run a GLM on a functional data set. % % Tested 01/04/2011 - MATLAB r2008a, Fedora 12, Current Repos % % Stanford VISTA %

%% Initialize the key variables and data path: % Data directory (where the mrSession file is located) dataDir = fullfile(mrvDataRootPath,'functional','vwfaLoc'); parfDir = fullfile(dataDir, 'Stimuli', 'parfiles');

% You must analyze with the matlab directory in the data directory. curDir = pwd; % We will put you back where you started at the end chdir(dataDir);

% There can be several data types - we're using motion compensated dated dataType = 'MotionComp';

%% Get data structure: vw = initHiddenInplane(); % Foregoes interface - loads data silently

%% Prepare scans for GLM

numScans = viewGet(vw, 'numScans'); whichScans = 1:numScans;

% If you're processing your own experiment, you'll need to produce parfiles % More info @ % http://white.stanford.edu/newIm/index.php/GLM#Create_.par_files_for_each_scan whichParfs = {'VWFALocalizer1.par' ... 'VWFALocalizer2.par' ... 'VWFALocalizer3.par'};

vw = er_assignParfilesToScans(vw, whichScans, whichParfs); % Assign parfiles to scans vw = er_groupScans(vw, whichScans, [], dataType); % Group scans together

%% Set GLM Parameters: % The GLM parameters are stored in a Matlab structure. % We call the structure params. % The parameters, such as params.timeWindow inform the GLM processing % routine about the experiment. % % A description of the parameters can be found on the wiki at: % % http://white.stanford.edu/newlm/index.php/MrVista_1_conventions#eventAnalysisParams params.timeWindow = -8:24; % params.bslPeriod = -8:0; % params.peakPeriod = 4:14; % params.framePeriod = 2; % TR params.normBsl = 1; params.onsetDelta = 0; params.snrConds = 1; params.glmHRF = 2; params.eventsPerBlock = 6; params.ampType = 'betas'; params.detrend = 1; params.detrendFrames = 20; params.inhomoCorrect = 1; params.temporalNormalization = 0; params.glmWhiten = 0;

saveToDataType = 'GLMs'; % Data type the results will be saved to

%% Run GLM: % Returns view structure and saved-to scan number in new data type [vw, newScan] = applyGlm(vw, dataType, whichScans, params, saveToDataType);

% newScan indicates the scan # in which results are saved % vw is a mrVista view structure. If you just type vw, you will see a lot % of the fields. In this case, many of them are empty. To understand what % the fields can represent, see the vistalab wiki re: GLMs.

%% To delete the new GLM run: removeScan(vw, newScan, saveToDataType, 1);

%% END

SOURCE END
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