Modifying analyzePixelIVF.m to run with Slicer generated segmentations

matlab/analyzePixelIVF.m

@@ -6,9 +6,15 @@ addpath('nrrd_read_write_rensonnet')
 
 [cax,cm]=loadTime(path,patientID);
 
-segmFile=fullfile(path,patientID,sprintf('%s_Segmentation.txt',patientID));
+%segmFile=fullfile(path,patientID,sprintf('%s_Segmentation.txt',patientID));
 %v0=loadPixels(segm,patientID);
-v0=dlmread(segmFile);
+[filepath,name,suffix]=fileparts(segmFile);
+if suffix=='nrrd'
+    v0=extractPixelsFromNrrd(segmFile);
+end
+if suffix=='txt'
+    v0=dlmread(segmFile);
+end
 
 data=loadSPECTdata(path,patientID,cm);
 

matlab/extractPixelsFromNrrd.m

@@ -0,0 +1,18 @@
+function v0=extractPixelsFromNrrd(file)
+%extract a nRegion x nx x ny x nz table where 
+%each point contained in segmentation corresponds to 
+%a row in output table v0
+    
+    addpath('nrrd_read_write_rensonnet')
+    hInfo=nhdr_nrrd_read(file,true);
+    v0=zeros(0,4);
+    for idx=1:10
+        f=find(hInfo.data==idx);
+        n=size(f,1)
+        if n==0
+            continue
+        end
+        [a,b,c]=ind2sub(size(hInfo.data),f);
+        v0=[v0; [idx*ones(n,1) a b c] ];
+        
+    end