Added copying of misc header info

volume.cc

@@ -93,35 +93,7 @@ namespace MISCMATHS {
     preThresholdPositions = preThresholdPositions.Rows(1,j);
   }
 
-//   void Volume::threshold(const volume<int>& pmask)
-//   {
-//     Time_Tracer ts("Volume::threshold");
 
-//     int size = getVolumeSize();
-//     int j = 0;
-       
-//     preThresholdPositions.ReSize(size);
-
-//     int i = 0;
-//     for(int x = 0; x < pmask.xsize(); x++)
-//       for(int y = 0; y < pmask.ysize(); y++)
-// 	for(int z = 0; z < pmask.zsize(); z++)
-// 	  {
-// 	    i++;
-// 	    if(pmask(x,y,z))
-// 	      {
-// 		j++;	
-// 		preThresholdPositions(j) = i;
-		   
-// 		(*this)(j) = (*this)(i);
-// 	      }
-// 	  }
-
-//     // Discard rest:
-//     *this = Rows(1,j);
-
-//     preThresholdPositions = preThresholdPositions.Rows(1,j);
-//   }
 
   void Volume::writeAsFloat(const string& fname)
   {    
@@ -131,10 +103,13 @@ namespace MISCMATHS {
     const ColumnVector& outputvol = *this;
     FSLIO* OP = FslOpen(fname.c_str(), "wb");
 
+    FslCloneHeader(OP,volinfo.miscinfo);
+   
     FslSetDim(OP,volinfo.x, volinfo.y, volinfo.z, 1);
     FslSetVoxDim(OP,volinfo.vx, volinfo.vy, volinfo.vz, 0);
     FslSetDataType(OP, DT_FLOAT);
-    FslSetOriginator(OP, volinfo.originator);
+    FslSetIntent(OP, volinfo.intent_code, volinfo.intent_p1, volinfo.intent_p2, 
+		 volinfo.intent_p3);
 
     int sizeVol = outputvol.Nrows();
 
@@ -154,8 +129,6 @@ namespace MISCMATHS {
 
     FslSetMinMax(OP, (short)fmin, (short)fmax);
 
-    //       fwrite(qv,sizeVol*sizeof(float),1,OP->imgfp);
-    //fwrite(&OP->header,sizeof(OP->header),1,OP->hdrfp);
     FslWriteHeader(OP);
     FslWriteVolumes(OP, qv, 1);
 
@@ -172,10 +145,13 @@ namespace MISCMATHS {
     const ColumnVector& outputvol = *this;
     FSLIO* OP = FslOpen(fname.c_str(), "wb");
  
+    FslCloneHeader(OP,volinfo.miscinfo);
+   
     FslSetDim(OP, volinfo.x, volinfo.y, volinfo.z, 1);  
     FslSetVoxDim(OP, volinfo.vx, volinfo.vy, volinfo.vz, 0);  
     FslSetDataType(OP, DT_SIGNED_SHORT);
-    FslSetOriginator(OP, volinfo.originator);
+    FslSetIntent(OP, volinfo.intent_code, volinfo.intent_p1, volinfo.intent_p2, 
+		 volinfo.intent_p3);
 
     int sizeVol = outputvol.Nrows();
 
@@ -218,12 +194,16 @@ namespace MISCMATHS {
 
     FslGetDim(IP,&x,&y,&z,&v);
     FslGetVoxDim(IP,&vx,&vy,&vz,&tr);
-    FslGetOriginator(IP,volinfo.originator);
+    FslGetIntent(IP, &(volinfo.intent_code), &(volinfo.intent_p1), &(volinfo.intent_p2), 
+		 &(volinfo.intent_p3));
     doscaling = FslGetIntensityScaling(IP,&slope,&intercept);
 
     volinfo.x = x; volinfo.y = y; volinfo.z = z; volinfo.v = v;
     volinfo.vx = vx; volinfo.vy = vy; volinfo.vz = vz; volinfo.tr = tr;
 
+    volinfo.miscinfo = FslInit();
+    FslCloneHeader(volinfo.miscinfo,IP);
+
     size_t imagesize=x*y*z;
     FslGetDataType(IP,&type);
   

volumeinfo.h

@@ -6,6 +6,8 @@
 
 /*  CCOPYRIGHT  */
 
+#include "fslio/fslio.h"
+
 namespace MISCMATHS {
   
 #if !defined(__VolumeInfo_h)
@@ -25,7 +27,13 @@ struct VolumeInfo
   float vz;
   float tr;
 
-  short originator[5];
+  // Intent codes and parameters
+  short intent_code;
+  float intent_p1;
+  float intent_p2;
+  float intent_p3;
+
+  FSLIO* miscinfo;
 };
 
 

volumeseries.cc

@@ -144,12 +144,16 @@ namespace MISCMATHS {
 
       FslGetDim(IP,&x,&y,&z,&v);
       FslGetVoxDim(IP,&vx,&vy,&vz,&tr);
-      FslGetOriginator(IP,volinfo.originator);
+      FslGetIntent(IP, &(volinfo.intent_code), &(volinfo.intent_p1), &(volinfo.intent_p2), 
+		   &(volinfo.intent_p3));
       doscaling = FslGetIntensityScaling(IP,&slope,&intercept);
 
       volinfo.x = x; volinfo.y = y; volinfo.z = z; volinfo.v = v;
       volinfo.vx = vx; volinfo.vy = vy; volinfo.vz = vz; volinfo.tr = tr;
 
+      volinfo.miscinfo = FslInit();
+      FslCloneHeader(volinfo.miscinfo,IP);
+
       size_t imagesize=x*y*z*v;
       FslGetDataType(IP,&type);
   
@@ -240,10 +244,13 @@ namespace MISCMATHS {
 
        FSLIO* OP = FslOpen(fname.c_str(), "wb");
 
+       FslCloneHeader(OP,volinfo.miscinfo);
+       
        FslSetDim(OP,volinfo.x, volinfo.y, volinfo.z, volinfo.v);
        FslSetVoxDim(OP,volinfo.vx, volinfo.vy, volinfo.vz, volinfo.tr);
        FslSetDataType(OP, DT_FLOAT);
-       FslSetOriginator(OP, volinfo.originator);
+       FslSetIntent(OP, volinfo.intent_code, volinfo.intent_p1, volinfo.intent_p2, 
+		    volinfo.intent_p3);
 
        int volStart = 1;
        int volSize = getNumSeries();