All MJ changes for LR2

miscmaths.h

@@ -181,6 +181,27 @@ namespace MISCMATHS {
   inline ReturnMatrix median(const Matrix& in){ return quantile(in,2);}
   inline ReturnMatrix iqr(const Matrix& in){ Matrix res = quantile(in,3) - quantile(in,1); res.Release(); return res;}
 
+// the following give left-right order and voxel2mm coordinate conversions
+//  consistent with FSLView behaviour (NB: you cannot tell left-right from
+//  the vox2mm matrix!)
+  int FslGetLeftRightOrder(int sform_code, const Matrix& sform_mat, 
+			   int qform_code, const Matrix& qform_mat);
+  short FslGetVox2mmMatrix(Matrix& vox2mm,
+			   int sform_code, const Matrix& sform_mat, 
+			   int qform_code, const Matrix& qform_mat, 
+			   float dx, float dy, float dz);
+  Matrix FslGetVox2VoxMatrix(const Matrix& flirt_in2ref,
+			     int sform_code_in, const Matrix& sform_mat_in, 
+			     int qform_code_in, const Matrix& qform_mat_in, 
+			     float dx_in, float dy_in, float dz_in,
+			     int nx_in, int ny_in, int nz_in,
+			     int sform_code_ref, const Matrix& sform_mat_ref, 
+			     int qform_code_ref, const Matrix& qform_mat_ref, 
+			     float dx_ref, float dy_ref, float dz_ref,
+			     int nx_ref, int ny_ref, int nz_ref);
+  mat44 newmat_to_mat44(const Matrix& inmat);
+  Matrix mat44_to_newmat(mat44 inmat);
+
   void cart2sph(const ColumnVector& dir, float& th, float& ph);// cartesian to sperical polar coordinates
   void cart2sph(const Matrix& dir,ColumnVector& th,ColumnVector& ph);//ditto
   void cart2sph(const vector<ColumnVector>& dir,ColumnVector& th,ColumnVector& ph);// same but in a vector