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Functions for exporting graph data (a list of connected nodes and corresponding attribute values) for functional neuroimaging data. Currently includes cytoscape and gephi. You must provide a list of anatomical labels (the variable AAL_labels).
function cytoscapeExport(links,weights,threshold,exptype)
% This function will take a list of links and weights, and create a file to
% import into Cytoscape for further graph analysis
% exptype is the export type - 'all' means voxelwise above a threshold,
% 'region' means creating graph of average regional values
% links is an n by 2 list of connections, each a voxel id
% weights is a correlation value corresponding to each link set
% You must load AAL_labels, a cell of length 116 with region names, and
% aalflat is a flattened AAL atlas, the same size as the original data
% First write sif file - this is a list of connections between nodes based
% on voxel index
if strcmp(exptype,'all')
voxels = unique(links(weights>threshold,:),'rows');
nodes = unique([ voxels(:,1) voxels(:,2) ]);
weightpt9 = weights(weights>threshold);
% Write each to file
filey = fopen('brain.sif','w');
for v=1:length(voxels)
fprintf(filey,'%s\n',[ num2str(voxels(v,1)) ' fc ' num2str(voxels(v,2)) ]);
end
fclose(filey);
% Now create data file that includes region names
filey = fopen('brain_features.csv','w');
fprintf(filey,'%s\n','VOXEL,REGION_AAL');
for n=1:length(nodes)
fprintf(filey,'%s\n',[ num2str(nodes(n)) ',' AAL_labels{aalflat(nodes(n))} ]);
end
fclose(filey);
% Write edges to file
filey = fopen('brain_edges.csv','w');
for v=1:length(voxels)
fprintf(filey,'%s\n',[ num2str(voxels(v,1)) ' (fc) ' num2str(voxels(v,2)) ' = ' num2str(weightpt9(v)) ]);
end
fclose(filey);
elseif strcmp(exptype,'region')
% Get unique links and weights
linksA = links(weights>threshold,:);
weightsA = weights(weights>threshold);
[linksA,ia,~] = unique(linksA,'rows');
weightsA = weightsA(ia);
% Now we need to get rid of duplicates, and also when i==j
linksAinv = [ linksA(:,2) linksA(:,1) ];
dups = (linksA == linksAinv);
linksA(dups(:,1),:) = [];
weightsA(dups(:,1)) = [];
% For each region, calculate mean weight
region_weights = cell(116,116);
region_vox = zeros(116,116);
for i=1:116
for j=1:116
region_weights{i,j} = [];
end
end
for l=1:length(linksA)
nodes = sort(aalflat(linksA(l,:)));
% If we have the same region
region_vox(nodes(1),nodes(2)) = region_vox(nodes(1),nodes(2)) + 1;
region_weights{nodes(1),nodes(2)} = [ region_weights{nodes(1),nodes(2)}; weightsA(l) ];
end
% Calculate mean inter and intra region weights
mean_weights = zeros(116,116);
for i=1:116
for j=1:116
weightset = region_weights{i,j};
mean_weights(i,j) = mean(weightset(~isnan(weightset)));
end
end
mean_weights(isnan(mean_weights)) = 0;
% Now write to cytoscape export file
filey = fopen('brain_region.sif','w');
for r1=1:116
for r2=1:116
region1 = AAL_labels{r1};
region2 = AAL_labels{r2};
fprintf(filey,'%s\n',[ region1 ' fc ' region2 ]);
end
end
fclose(filey);
% Now create data file that includes intra region weights
filey = fopen('brain_region_features.csv','w');
for w1=1:size(mean_weights,1)
for w2=1:size(mean_weights,2)
if w1==w2
region1 = AAL_labels{w1};
fprintf(filey,'%s\n',[ region1 ',' num2str(mean_weights(w1,w2)) ]);
end
end
end
fclose(filey);
% Write iter region weights (edges) to file
filey = fopen('brain_region_edges.csv','w');
for w1=1:size(mean_weights,1)
for w2=1:size(mean_weights,2)
if w1~=w2
region1 = AAL_labels{w1};
region2 = AAL_labels{w2};
if mean_weights(w1,w2) ~= 0
fprintf(filey,'%s\n',[ region1 ' (fc) ' region2 ' = ' num2str(mean_weights(w1,w2)) ]);
end
end
end
end
fclose(filey);
else
error('Invalid export type - must specify all or region for fourth argument!');
end
function gephiExport(links,weights,threshold)
% This function will take a list of links and weights, and create a file to
% import into gephi for further graph analysis
% links is an n by 2 list of connections, each a voxel id
% weights is a correlation value corresponding to each link set
% You must load AAL_labels, a cell of length 116 with region names, and
% aalflat is a flattened AAL atlas, the same size as the original data
% Get unique links and weights
linksA = links(weights>threshold,:);
weightsA = weights(weights>threshold);
[linksA,ia,~] = unique(linksA,'rows');
weightsA = weightsA(ia);
% Now we need to get rid of duplicates, and also when i==j
linksAinv = [ linksA(:,2) linksA(:,1) ];
dups = (linksA == linksAinv);
linksA(dups(:,1),:) = [];
weightsA(dups(:,1)) = [];
% For each region, calculate mean weight
region_weights = cell(116,116);
region_vox = zeros(116,116);
for i=1:116
for j=1:116
region_weights{i,j} = [];
end
end
for l=1:length(linksA)
nodes = sort(aalflat(linksA(l,:)));
% If we have the same region
region_vox(nodes(1),nodes(2)) = region_vox(nodes(1),nodes(2)) + 1;
region_weights{nodes(1),nodes(2)} = [ region_weights{nodes(1),nodes(2)}; weightsA(l) ];
end
% Calculate mean inter and intra region weights
mean_weights = zeros(116,116);
for i=1:116
for j=1:116
weightset = region_weights{i,j};
mean_weights(i,j) = mean(weightset(~isnan(weightset)));
end
end
mean_weights(isnan(mean_weights)) = 0;
% Now write to graph wiz export file
filey = fopen('brain_region.gexf','w');
fprintf(filey,'%s\n%s\n%s\n%s\n','<gexf xmlns:viz="http:///www.gexf.net/1.1draft/viz" xmlns="http://www.gexf.net/1.1draft" version="1.1">','<meta lastmodifieddate="2010-03-03+23:44">','<creator>Gephi 0.7</creator>','</meta>','<graph defaultedgetype="undirected" idtype="string" type="static">');
fprintf(filey,'%s\n',[ '<nodes count="' num2str(length(AAL_labels)) '">' ]);
for r1=1:116
fprintf(filey,'%s\n',[ 'node id="' num2str(i) '" label="' AAL_labels{r1} '">' ]);
end
fprintf(filey,'%s\n%s\n','</nodes>',[ '<edges count="' num2str(length(links)) '">' ]);
edge_count = 0;
for r1=1:116
for r2=1:116
region1 = AAL_labels{r1};
region2 = AAL_labels{r2};
if mean_weights(r1,r2) ~= 0
fprintf(filey,'%s\n',[ '<edge id="' num2str(edge_count) '" source="' num2str(r1) '" target="' num2str(r2) '" weight="' num2str(mean_weights(r1,r2)) '"/>' ]);
edge_count = edge_count + 1;
end
end
end
fprintf(filey,'%s\n%s\n%s\n','</edges>','</graph>','</gexf>');
fclose(filey);
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