More outline options, helper functions

- changed default line/edge properties for outlined overlays to minimize some visual artifacts on windows
- added two new contextual menus for changing line/edge properties for outlined overlays and atlases  (right click outline dropdown menu for overlays or outline toggle for atlas to summon the new GUI)
-writeDataToAtlas in misc. scripts directory can help you assign values to individual ROIs in an atlas (e.g., based on some statistical tests)

Author: alexteghipco

GUIs/outProp.mlapp

@@ -0,0 +1,54 @@
+function writeDataToAtlas(atLabs,atFile,data,dataLabs,ofAppend)
+% This function will take an atlas file and write in new values for each
+% ROI in the atlas. 
+%
+% atLabs: a text file showing labels for each ROI. See
+% jhu_resampled_to_FSL_fixed_noWM as an example
+%
+% atFile: a path to a nifti file
+%
+% data: an n x 1 matrix where n corresponds to number of ROIs
+%
+% dataLabs: an n x 1 matrix where n corresponds to the name of the ROI,
+% which must match the names in atLabs. Note, each row in dataLabs has to
+% correspond to the same region as the row in data. 
+% 
+% example call: writeDataToAtlas('D:\Science\Matlab\GitHub\brainSurfer\atlases\jhu_resampled_to_FSL_fixed_noWM.txt',{'D:\Science\Matlab\GitHub\brainSurfer\atlases\jhu_resampled_to_FSL_fixed_noWM_renamed_CombinedClusters_FSSpace_LH.nii.gz';'D:\Science\Matlab\GitHub\brainSurfer\atlases\jhu_resampled_to_FSL_fixed_noWM_renamed_CombinedClusters_FSSpace_RH.nii.gz'},[0.2; 0.2],{'MTG L cbf ','Cu L cbf'})
+
+atLabs = readtable(atLabs);
+atNii{1} = load_nifti(atFile{1});
+atNii{2} = load_nifti(atFile{2});
+
+of{1} = atNii{1};
+of{1}.vol = zeros(size(of{1}.vol));
+of{2} = atNii{2};
+of{2}.vol = zeros(size(of{2}.vol));
+
+for i = 1:length(data)
+    id = strfind(dataLabs{i},' ');
+    if contains(dataLabs{i},'pole')
+        tmp = dataLabs{i}(1:id(end)-(id(end)-id(end-1))-1);
+    else
+        tmp = dataLabs{i}(1:id(end)-(id(end)-id(end-2)-1)); %dataLabs{i}(1:id(end)-5);
+    end
+
+    id = strfind(tmp,' ');
+    tmp(id) = '_';
+    id = find(ismember(atLabs.Var2,tmp));
+    if isempty(id)
+        disp([dataLabs{i} ' not found'])
+    else
+        id = atLabs.Var1(id);
+        c1 = intersect(atNii{1}.vol,id);
+        c2 = intersect(atNii{2}.vol,id);
+        if ~isempty(c1)
+            mid = find(atNii{1}.vol == id);
+            of{1}.vol(mid) = data(i);
+        elseif ~isempty(c2)
+            mid = find(atNii{2}.vol == id);
+            of{2}.vol(mid) = data(i);
+        end
+    end
+end
+save_nifti(of{1},[atFile{1}(1:end-7) ofAppend '.nii.gz'])
+save_nifti(of{2},[atFile{2}(1:end-7) ofAppend '.nii.gz'])