Suppress background noise when estimating FA for multimodal normaliza…

…tion.
netstim · May 4, 2016 · d409bf0 · d409bf0
1 parent 3a9f354
commit d409bf0
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Showing 3 changed files with 4 additions and 6 deletions.
diff --git a/connectomics/ea_isolate_fa.m b/connectomics/ea_isolate_fa.m
@@ -27,7 +27,7 @@ function ea_isolate_fa(directory,options)
 
 % Constants DTI
 parametersDTI=[];
-parametersDTI.BackgroundTreshold=150;
+parametersDTI.BackgroundThreshold=150;
 parametersDTI.WhiteMatterExtractionThreshold=0.10;
 parametersDTI.textdisplay=true;
 

diff --git a/ext_libs/ftracking/ea_DTI.m b/ext_libs/ftracking/ea_DTI.m
@@ -6,7 +6,7 @@
 %
 % DTIdata:  A struct containing DTIdata(i).VoxelData, DTIdata(i).Gradient
 %           and DTIdata(i).Bvalue of all the DTI datasets
-% parameters: A struct containing, parameters.BackgroundTreshold and
+% parameters: A struct containing, parameters.BackgroundThreshold and
 %           parameters.WhiteMatterExtractionThreshold, parameters.textdisplay
 %
 % ADC: A 3D matrix with the Apparent Diffuse Coefficient (ADC)
@@ -96,7 +96,7 @@
         for z=1:size(S0,3),
 
             % Only process a pixel if it isn't background
-            %if(S0(x,y,z)>parameters.BackgroundTreshold)
+            if(S0(x,y,z)>parameters.BackgroundThreshold)
 
                 % Calculate the Diffusion tensor [Dxx,Dxy,Dxz,Dyy,Dyz,Dzz],
                 % with a simple matrix inverse.
@@ -142,7 +142,7 @@
                 if(FAv>parameters.WhiteMatterExtractionThreshold)
                     VectorF(x,y,z,:)=EigenVectors(:,end)*EigenValues_old(end);
                 end
-            %end
+            end
         end
     end
 end

diff --git a/lead.m b/lead.m
@@ -1215,13 +1215,11 @@ function ea_switchctmr(varargin)
             set(handles.coregctcheck,'Enable','off');
             set(handles.coregctcheck,'Value',0);
             set(handles.coregthreshs,'Enable','off');
-            set(handles.coregmrpopup,'Enable','on');
         case 2 % CT
             set(handles.coregct_checkbox,'Enable','on');
             set(handles.coregctmethod,'Enable','on');
             set(handles.coregctcheck,'Enable','on');
             set(handles.coregthreshs,'Enable','on');
-            set(handles.coregmrpopup,'Enable','off');
     end
 end
 updatestatus(handles);