masks no longer have to binary. bvecs no longer have to be normalised. bvecs...

 masks no longer have to binary. bvecs no longer have to be normalised. bvecs and bvals can be horizontal or vertical matrices

dtifit.cc

@@ -187,7 +187,15 @@ int main(int argc, char** argv)
   
   // Set random seed:
   Matrix r = read_ascii_matrix(opts.bvecsfile.value());
+  if(r.Nrows()>3) r=r.t();
+  for(int i=1;i<=r.Ncols();i++){
+    float tmpsum=sqrt(r(i,1)*r(i,1)+r(i,2)*r(i,2)+r(i,3)*r(i,3));
+    r(i,1)=r(i,1)/tmpsum;
+    r(i,2)=r(i,2)/tmpsum;
+    r(i,3)=r(i,3)/tmpsum;
+  }
   Matrix b = read_ascii_matrix(opts.bvalsfile.value());
+  if(b.Nrows()>1) b=b.t();
   volume4D<float> data;
   volume<int> mask;
   volumeinfo tempinfo;
@@ -238,12 +246,11 @@ int main(int argc, char** argv)
       for(int j=miny; j < maxy; j++){
 	for(int i =minx; i< maxx; i++){
 	
-	  if(mask(i,j,k)==1){
+	  if(mask(i,j,k)>0){
 	    
 	    for(int t=0;t < data.tsize();t++){
 	      S(t+1)=data(i,j,k,t);
 	    }
-	   
 	    tensorfit(evals,evec1,evec2,evec3,fa,s0,Amat,S);
 	    l1(i-minx,j-miny,k-minz)=evals(1);
 	    l2(i-minx,j-miny,k-minz)=evals(2);