*** empty log message ***

ContrastMgr.cc

@@ -211,7 +211,7 @@ namespace FILM {
    
     VolumeInfo tmpinfo;
 
-    // Write out tstat:
+    // Write out fstat:
     tmpinfo = sigmaSquareds.getInfo();
     tmpinfo.intent_code = NIFTI_INTENT_FTEST;
     tmpinfo.intent_p1 = 0.0;
@@ -244,6 +244,7 @@ namespace FILM {
 
     // Write out neffs:
     tmpinfo = sigmaSquareds.getInfo();
+    tmpinfo.intent_code = NIFTI_INTENT_NONE;
     neff.setInfo(tmpinfo);
     neff.setPreThresholdPositions(sigmaSquareds.getPreThresholdPositions());
     neff.unthreshold();
@@ -251,7 +252,7 @@ namespace FILM {
 
     // Write out cope:
     tmpinfo = sigmaSquareds.getInfo();
-    tmpinfo.intent_code = NIFTI_INTENT_CORREL;
+    tmpinfo.intent_code = NIFTI_INTENT_ESTIMATE;
     tmpinfo.intent_p1 = 0.0;
     cb.setInfo(tmpinfo);
     cb.setPreThresholdPositions(sigmaSquareds.getPreThresholdPositions());
@@ -260,7 +261,7 @@ namespace FILM {
 
     // Write out varcope:
     tmpinfo = sigmaSquareds.getInfo();
-    tmpinfo.intent_code = NIFTI_INTENT_CHISQ;
+    tmpinfo.intent_code = NIFTI_INTENT_ESTIMATE;
     tmpinfo.intent_p1 = 0.0;
     varcb.setInfo(tmpinfo);
     varcb.setPreThresholdPositions(sigmaSquareds.getPreThresholdPositions());

film_gls.cc

@@ -214,6 +214,7 @@ int main(int argc, char *argv[])
     threshac = threshac.Rows(1,cutoff);
     VolumeInfo volinfo = x.getInfo();
     volinfo.v = cutoff;
+    volinfo.intent_code = NIFTI_INTENT_ESTIMATE;
     threshac.unthresholdSeries(volinfo,x.getPreThresholdPositions());
     threshac.writeAsFloat(logger.getDir() + "/threshac1");
     threshac.thresholdSeries();

ftoz.cc

@@ -129,7 +129,10 @@ int main(int argc,char *argv[])
     Volume zs(numTS);
     F2z::ComputeFStats(fs, globalopts.dof1, globalopts.dof2, zs);
    
-    zs.setInfo(fs.getInfo());
+    VolumeInfo volinfo = fs.getInfo();
+    volinfo.intent_code = NIFTI_INTENT_ZSCORE;
+    volinfo.intent_p1 = 0.0;    
+    zs.setInfo(volinfo);
     zs.writeAsFloat(globalopts.zscoresfname.c_str());
   }
   catch(Exception p_excp) 

glimGls.cc

@@ -47,16 +47,19 @@ namespace FILM {
       SetCorrection(inv_xx, ind);
     }
 
-  void GlimGls::Save(const VolumeInfo& volinfo, const ColumnVector& prethreshpos)
+  void GlimGls::Save(const VolumeInfo& pvolinfo, const ColumnVector& prethreshpos)
     {
       // Need to save b, sigmaSquareds, corrections and dof 
       Log& logger = LogSingleton::getInstance();
 
+      VolumeInfo volinfo = pvolinfo;
+
       // b:
       Volume peVol;
       for(int i = 1; i <= numParams; i++)
 	{
 	  peVol = b.Row(i).AsColumn();
+	  volinfo.intent_code = NIFTI_INTENT_ESTIMATE;
 	  peVol.setInfo(volinfo);
 	  peVol.setPreThresholdPositions(prethreshpos);
 	  peVol.unthreshold();
@@ -70,6 +73,7 @@ namespace FILM {
 	}
 
       // sigmaSquareds:
+      volinfo.intent_code = NIFTI_INTENT_ESTIMATE;
       sigmaSquareds.setInfo(volinfo);
       sigmaSquareds.setPreThresholdPositions(prethreshpos);
       sigmaSquareds.unthreshold();	
@@ -83,6 +87,7 @@ namespace FILM {
       // corrections (are the pes correlation matrix (x.t()*x).i() reshapen to a vector):
       VolumeInfo newvolinfo = volinfo;
       newvolinfo.v = numParams*numParams;
+      newvolinfo.intent_code = NIFTI_INTENT_NONE;
       corrections.setInfo(newvolinfo);
       corrections.setPreThresholdPositions(prethreshpos);
       corrections.unthresholdSeries();

ttologp.cc

@@ -132,7 +132,9 @@ int main(int argc,char *argv[])
     Volume ps(numTS);
     T2z::ComputePs(vars, cbs, globalopts.dof, ps);
     
-    ps.setInfo(vars.getInfo());
+    VolumeInfo volinfo = vars.getInfo();
+    volinfo.intent_code = NIFTI_INTENT_LOGPVAL;
+    ps.setInfo(volinfo);
     ps.writeAsFloat(globalopts.logpfname.c_str());
   }
   catch(Exception p_excp) 

ttoz.cc

@@ -130,9 +130,13 @@ int main(int argc,char *argv[])
 
     Volume zs(numTS);
     T2z::ComputeZStats(vars, cbs, globalopts.dof, zs);
-    
-    zs.setInfo(vars.getInfo());
+
+    VolumeInfo volinfo = vars.getInfo();
+    volinfo.intent_code = NIFTI_INTENT_ZSCORE;
+    volinfo.intent_p1 = 0.0;    
+    zs.setInfo(volinfo);
     zs.writeAsFloat(globalopts.zscoresfname.c_str());
+
   }
   catch(Exception p_excp) 
     {