updating documentation

Allen_to_GroupSpace.m

@@ -1,6 +1,13 @@
 function Allen_to_GroupSpace(Templates)
 
-% ------ Transformation of ANO to group template space ------ % 
+% Description: Transformation of ANO file to group template space 
+% -----------------------------------------%
+% Tanusree Chaudhuri
+% Max Planck Institute of Psychiatry, Munich
+% tanusree_chaudhuri@psych.mpg.de
+% -----------------------------------------%
+
+% ----------------------------------------------------------------------------------------%
 global DataDir;
 global TemplatesDir;
 

ClusterLabelling.m

@@ -1,5 +1,14 @@
 
 function [ClusterLabels, ClusterParents] = ClusterLabelling(ClusterIntensities,ANO)
+
+% Description: Labelling detected brain regions in each cluster blob in the
+% cluster image. 
+
+% -----------------------------------------%
+% Tanusree Chaudhuri
+% Max Planck Institute of Psychiatry, Munich
+% tanusree_chaudhuri@psych.mpg.de
+% -----------------------------------------%
 Region = table2array(ANO(:,1));
 ID = table2array(ANO(:,4));
 colHex = table2array(ANO(:,2));

Cluster_Overlap_main.m

@@ -1,20 +1,22 @@
 function [ClusterTable] = Cluster_Overlap_main(ImageFiles)
+% %----Description----%
+% Run this script to obtain proportion of brain regions detected in the cluster images. 
 
-%%%% ----- Cluster Overlap Task ----- %%%%
-%---------------------------------------------------------------------------------------------------------------%
-% Documentation: Run this script to obtain proportion of brain
-% regions detected in the cluster images. The output will appear in the
-% command window as the number of clusters detected
-% and the proportion (in percentage) of different brain regions present in
-% each cluster.
-% 'CodeDir' contains the fullpath to the folder into which the Toolbox is copied.
-% 'DataDir' is the fullpath to the directory whose data needs to be analysed
-% by this pipeline.
+% FORMAT [ClusterTable] = Cluster_Overlap_main(ImageFiles)
+% 
+% %----Input----%
+% ImageFiles: Filename of cluster image. 
+
+% %----Output----%
+% ClusterTable: Table array showing percentages and parent regions of
+% detected brain regions in each cluster blob. 
 %
 % -----------------------------------------%
 % Tanusree Chaudhuri
 % Max Planck Institute of Psychiatry, Munich
+% tanusree_chaudhuri@psych.mpg.de
 % -----------------------------------------%
+
 %---------------------------------------------------------------------------------------------------------------%
 
 global DataDir;

Cluster_Overlap_main.m~

@@ -0,0 +1,88 @@
+function [ClusterTable] = Cluster_Overlap_main(ImageFiles)
+
+%%%% ----- Cluster Overlap Task ----- %%%%
+%---------------------------------------------------------------------------------------------------------------%
+
+% 'CodeDir' contains the fullpath to the folder into which the Toolbox is copied.
+% 'DataDir' is the fullpath to the directory whose data needs to be analysed
+% by this pipeline.
+%
+% %----Description----%
+% Run this script to obtain proportion of brain regions detected in the cluster images. 
+
+% FORMAT [ClusterTable] = Cluster_Overlap_main(ImageFiles)
+% 
+% %----Input----%
+% ImageFiles: Filename of cluster image. 
+
+% %----Output----%
+% ClusterTable: Table array showing per
+%
+% -----------------------------------------%
+% Tanusree Chaudhuri
+% Max Planck Institute of Psychiatry, Munich
+% tanusree_chaudhuri@psych.mpg.de
+% -----------------------------------------%
+
+%---------------------------------------------------------------------------------------------------------------%
+
+global DataDir;
+global TemplatesDir;
+
+cd(DataDir);
+
+% ----- Binarizing cluster image ------ %
+ImagesToBeMasked = ImageFiles;
+InputFilename = cellstr(ImagesToBeMasked);
+[pth,nam,ext] = spm_fileparts(ImageFiles);
+OutputFilename = strcat(pth,'/Mask_',nam,ext);
+MaskingClusterImages(InputFilename,OutputFilename);
+
+% ------ Cluster Labelling.------ %
+ClusterMask = spm_vol(OutputFilename);
+ClusterMask = spm_read_vols(ClusterMask);
+CC = bwconncomp(ClusterMask);
+NumberOfClusters = CC.NumObjects;
+
+
+for img_cluster = 1:NumberOfClusters
+
+    [ClusterLabels,ClusterParents,ClusterLabelsPercent] = ClusterProportionInPercentages(TemplatesDir,CC,img_cluster);
+    if(isempty(ClusterLabels))
+        Cluster_blob_num = cellstr(repmat(['Cluster',' ',num2str(img_cluster)],[1, 1]));
+        ClusterLabels{end + 1} = [];
+        ClusterLabelsPercent = 100;
+        ClusterParents{end + 1} = [];
+    end
+    Cluster_blob_num = cellstr(repmat(['Cluster',' ',num2str(img_cluster)],[length(ClusterLabels) 1]));
+    ClusterParents = ClusterParents';
+    ClusterImageInfo = table(Cluster_blob_num,ClusterLabels,ClusterParents,ClusterLabelsPercent);
+    disp(strcat('Blob','_',num2str(img_cluster),'_','done'));
+
+
+    if(img_cluster == 1)
+        ClusterTable = ClusterImageInfo;
+    else
+        ClusterTable = [ClusterTable;ClusterImageInfo];
+    end
+
+end
+
+
+
+end
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

Start_ARET.m

@@ -1,4 +1,14 @@
 %%% ------ START ARET ------ %%%%
+% ------------------------------ %
+
+% Description: start Allen ROI Extraction Toolbox to perform two
+% functionalities - ROI Extraction and Cluster Labelling. 
+
+% -----------------------------------------%
+% Tanusree Chaudhuri
+% Max Planck Institute of Psychiatry, Munich
+% tanusree_chaudhuri@psych.mpg.de
+% -----------------------------------------%
 
 %% ----- Variables to be changed before running this script ----- %%%
 

annotation_tan.m

@@ -2,42 +2,30 @@
 function [Int_ROI,ROI] = annotation_tan(brain_region)
 
 % %----Description----%
-% Create masks of user specified gray matter regions using the latest antx templates,
-% specifically the annotation template(ANO.nii) and the allen table. 
-% Both files are located in TemplatesDir directory. 
+% Create masks of user specified brain regions using the annotation
+% template(ANO.nii) and the allen table in the templates folder. 
 
-% FORMAT [Int,mask,idxLUT] = annotation_tan(brain_region)
+% FORMAT [Int_ROI,ROI] = annotation_tan(brain_region)
 % 
 % %----Input----%
-% DataDir: fullpath to the directory with the cluster data. 
-% TemplatesDir = fullpath to the templates directory, which contains the
-% latest templates from the following link: 
-% https://drive.google.com/drive/folders/1q5XOOVLvUYLqYsQJLqNRF7OK8fNwYhI9
 % brain_region: name of brain region whose mask will be generated by this
 % function.
 % Please refer to manual to know how to give brain_region as an input. 
 
 % %----Output----%
 % Int: the allen intensities present in brain_region
-% mask: image volume of brain_region
+% ROI: image volume of brain_region
 %
 % -----------------------------------------%
 % Tanusree Chaudhuri
 % Max Planck Institute of Psychiatry, Munich
+% tanusree_chaudhuri@psych.mpg.de
 % -----------------------------------------%
 
 
-%global DataDir
 global TemplatesDir
 global ROI_ResultsDir
 
-% % ---- Creating subfolder for output images ---- %
-% cd(DataDir);
-% % if ~exist('ROI_Masks', 'dir')
-% %     mkdir('ROI_Masks')
-% % end
-% mkdir(ROI_ResultsDir);
-
 % ---------- 1.  ANO table  ------------ %%%%%
 ANO = readtable(strcat(TemplatesDir,'/ANO.xlsx'));
 Regions = table2array(ANO(:,1));