Working version with intents - hopefully

ContrastMgr.cc

@@ -17,6 +17,7 @@
 #include "miscmaths/f2z.h"
 #include "paradigm.h"
 #include "utils/tracer_plus.h"
+#include "fslio/fslio.h"
 
 using namespace Utilities;
 using namespace MISCMATHS;
@@ -208,14 +209,22 @@ namespace FILM {
     ostrstream osc(strc,50);
     osc << suffix << c_counter << '\0';
    
+    VolumeInfo tmpinfo;
+
     // Write out tstat:
-    fstat.setInfo(sigmaSquareds.getInfo());
+    tmpinfo = sigmaSquareds.getInfo();
+    tmpinfo.intent_code = NIFTI_INTENT_FTEST;
+    tmpinfo.intent_p1 = 0.0;
+    fstat.setInfo(tmpinfo);
     fstat.setPreThresholdPositions(sigmaSquareds.getPreThresholdPositions());
     fstat.unthreshold();
     fstat.writeAsFloat(logger.getDir() + "/fstat" + strc);
 
     // Write out zstat:
-    zstat.setInfo(sigmaSquareds.getInfo());
+    tmpinfo = sigmaSquareds.getInfo();
+    tmpinfo.intent_code = NIFTI_INTENT_ZSCORE;
+    tmpinfo.intent_p1 = 0.0;
+    zstat.setInfo(tmpinfo);
     zstat.setPreThresholdPositions(sigmaSquareds.getPreThresholdPositions());
     zstat.unthreshold();
     zstat.writeAsFloat(logger.getDir() + "/zfstat" + strc);
@@ -231,32 +240,47 @@ namespace FILM {
     ostrstream osc(strc,50);
     osc << suffix << c_counter << '\0';
 
+    VolumeInfo tmpinfo;
+
     // Write out neffs:
-    neff.setInfo(sigmaSquareds.getInfo());
+    tmpinfo = sigmaSquareds.getInfo();
+    neff.setInfo(tmpinfo);
     neff.setPreThresholdPositions(sigmaSquareds.getPreThresholdPositions());
     neff.unthreshold();
     neff.writeAsFloat(logger.getDir() + "/neff" + strc);
 
     // Write out cope:
-    cb.setInfo(sigmaSquareds.getInfo());
+    tmpinfo = sigmaSquareds.getInfo();
+    tmpinfo.intent_code = NIFTI_INTENT_CORREL;
+    tmpinfo.intent_p1 = 0.0;
+    cb.setInfo(tmpinfo);
     cb.setPreThresholdPositions(sigmaSquareds.getPreThresholdPositions());
     cb.unthreshold();
     cb.writeAsFloat(logger.getDir() + "/cope" + strc);
 
     // Write out varcope:
-    varcb.setInfo(sigmaSquareds.getInfo());
+    tmpinfo = sigmaSquareds.getInfo();
+    tmpinfo.intent_code = NIFTI_INTENT_CHISQ;
+    tmpinfo.intent_p1 = 0.0;
+    varcb.setInfo(tmpinfo);
     varcb.setPreThresholdPositions(sigmaSquareds.getPreThresholdPositions());
     varcb.unthreshold();
     varcb.writeAsFloat(logger.getDir() + "/varcope" + strc);
 
     // Write out tstat:
-    tstat.setInfo(sigmaSquareds.getInfo());
+    tmpinfo = sigmaSquareds.getInfo();
+    tmpinfo.intent_code = NIFTI_INTENT_TTEST;
+    tmpinfo.intent_p1 = 0.0;
+    tstat.setInfo(tmpinfo);
     tstat.setPreThresholdPositions(sigmaSquareds.getPreThresholdPositions());
     tstat.unthreshold();
     tstat.writeAsFloat(logger.getDir() + "/tstat" + strc);
 
     // Write out zstat:
-    zstat.setInfo(sigmaSquareds.getInfo());
+    tmpinfo = sigmaSquareds.getInfo();
+    tmpinfo.intent_code = NIFTI_INTENT_ZSCORE;
+    tmpinfo.intent_p1 = 0.0;
+    zstat.setInfo(tmpinfo);
     zstat.setPreThresholdPositions(sigmaSquareds.getPreThresholdPositions());
     zstat.unthreshold();
     zstat.writeAsFloat(logger.getDir() + "/zstat" + strc);