<code - 3_prepData_create_mask.m>

%
%   _______________________________________________
%   by Marcelo G Mattar (10/21/2013)
%   mattar@sas.upenn.edu
%
dataset = 'MDS_Multi';
masksize = 800;

load('~/Data/FaceSpace/ROIs/fusiform.mat')
rh = logical(rh);
lh = logical(lh);
[sig_rh, M_rh, mr_parms_rh] = load_mgh(['~/Data/FaceSpace/group_glms/' dataset '/DriftMainEffect/rh.DriftMainEffect.glmdir/osgm/sig.mgh']);
[sig_lh, M_lh, mr_parms_lh] = load_mgh(['~/Data/FaceSpace/group_glms/' dataset '/DriftMainEffect/lh.DriftMainEffect.glmdir/osgm/sig.mgh']);

% Initialize mask vectors
temp_rh = nan(size(sig_rh));
temp_lh = nan(size(sig_lh));
mainEffectMask_rh = nan(size(sig_rh));
mainEffectMask_lh = nan(size(sig_lh));

% Mask with the fusiform anatomical mask
temp_rh(rh) = sig_rh(rh);
temp_lh(lh) = sig_lh(lh);

% Find the index of the top vertices
temp_rh(isnan(temp_rh)) = -Inf;
temp_lh(isnan(temp_lh)) = -Inf;
[~,sorted_indices_rh] = sort(temp_rh,1,'descend');
[~,sorted_indices_lh] = sort(temp_lh,1,'descend');

% Create the masked vector
mainEffectMask_rh(sorted_indices_rh(1:masksize)) = temp_rh(sorted_indices_rh(1:masksize));
mainEffectMask_lh(sorted_indices_lh(1:masksize)) = temp_lh(sorted_indices_lh(1:masksize));

% Create binary mask
mask_rh = zeros(size(sig_rh));
mask_lh = zeros(size(sig_lh));
mask_rh(~isnan(mainEffectMask_rh)) = 1;
mask_lh(~isnan(mainEffectMask_lh)) = 1;
mask_rh = logical(mask_rh);
mask_lh = logical(mask_lh);

% Save output
save_mgh(mainEffectMask_rh,['~/Data/FaceSpace/ROIs/maskedBetas_' dataset '_' num2str(masksize) '_rh.mgh'],M_rh,mr_parms_rh);
save_mgh(mainEffectMask_lh,['~/Data/FaceSpace/ROIs/maskedBetas_' dataset '_' num2str(masksize) '_lh.mgh'],M_lh,mr_parms_lh);
save_mgh(mask_rh,['~/Data/FaceSpace/ROIs/binaryMask_' dataset '_' num2str(masksize) '_rh.mgh'],M_rh,mr_parms_rh);
save_mgh(mask_lh,['~/Data/FaceSpace/ROIs/binaryMask_' dataset '_' num2str(masksize) '_lh.mgh'],M_lh,mr_parms_lh);

</code>