whirlgif

fslanimate

@@ -56,12 +56,12 @@ $FSLDIR/bin/avwsplit $im
 for fnm in `$FSLDIR/bin/imglob vol*` ; do
   num=`$FSLDIR/bin/remove_ext $fnm | sed 's/vol//'`;  export num;
   echo $num; 
-  $FSLDIR/bin/slicer $fnm -s 2 -a ${iout}_$num.pgm
-  ${FSLCONVERT} ${iout}_$num.pgm ${iout}_$num.gif
-  rm -f ${iout}_$num.pgm
+  $FSLDIR/bin/slicer $fnm -s 2 -a ${iout}_$num.png
+  ${FSLDIR}/bin/pngappend ${iout}_$num.png ${iout}_$num.gif
+  rm -f ${iout}_$num.png
 done
 
-$FSLDIR/bin/gifmerge -15 -l0 ${iout}_*.gif > ${iout}.gif
+$FSLDIR/bin/whirlgif -o ${iout}.gif -time 15 -loop 0 ${iout}_*.gif
 
 mv $tmpdir/${iout}.gif ${imoutdir}/${iout}.gif
 

fslstats.cc

@@ -20,6 +20,12 @@ bool masks_used=false;
 bool lthr_used=false;
 bool uthr_used=false;
 
+#if defined ( __CYGWIN__ ) ||  defined (__sun)
+extern "C" { 
+#include <ieeefp.h> //for finite
+}
+#endif
+
 void print_usage(const string& progname) {
   cout << "Usage: avwstats++ <input> [options]" << endl << endl;
   cout << endl;
@@ -43,6 +49,7 @@ void print_usage(const string& progname) {
   cout << "-p <n>       : output nth percentile (n between 0 and 100)" << endl;
   cout << "-P <n>       : output nth percentile (for nonzero voxels)" << endl;
   cout << "-a           : use absolute values of all image intensities"<< endl;
+  cout << "-n           : treat NaN or Inf as zero for subsequent stats" << endl;
   cout << "-k <mask>    : use the specified image (filename) for masking - overrides lower and upper thresholds" << endl;
   cout << "-h <nbins>   : output a histogram (for the thresholded/masked voxels only) with nbins" << endl; 
   cout << "-H <nbins> <min> <max>   : output a histogram (for the thresholded/masked voxels only) with nbins and histogram limits of min and max" << endl; 
@@ -160,8 +167,14 @@ int fmrib_main_float(int argc, char* argv[])
  
   while (narg<argc) {
     sarg=argv[narg];
-
-    if (sarg=="-m") {
+    if (sarg=="-n") {
+      for (int t=vol.mint(); t<=vol.maxt(); t++)
+        for (int z=vol.minz(); z<=vol.maxz(); z++)
+          for (int y=vol.miny(); y<=vol.maxy(); y++)
+            for (int x=vol.minx(); x<=vol.maxx(); x++)
+              if (!finite((double)vol(x,y,z,t)))
+	        vol(x,y,z,t)=0;
+    } else if (sarg=="-m") {
       if (masks_used) cout <<  vol.mean(mask) << " ";
       else cout << vol.mean() << " ";
     } else if (sarg=="-M") {

sliceanimate

@@ -2,9 +2,9 @@
 
 #   sliceanimate - make animated gif of a volume, slice at a time
 #
-#   Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+#   Stephen Smith, Mark Jenkinson and Matthew Webster FMRIB Image Analysis Group
 #
-#   Copyright (C) 1999-2004 University of Oxford
+#   Copyright (C) 1999-2007 University of Oxford
 #
 #   SHCOPYRIGHT
 
@@ -25,16 +25,16 @@ tmpdir=/tmp
 
 while [ $n -lt $nn ] ; do
   # echo $FSLDIR/bin/slicer $volname $@ -z -$n $tmpdir/${tmpnam}
-  $FSLDIR/bin/slicer $volname $@ -z -$n $tmpdir/${tmpnam}
+  $FSLDIR/bin/slicer $volname $@ -z -$n $tmpdir/${tmpnam}.png
   snum=`echo "0000${n}" | sed 's/^.*\(....\)$/\1/'`;
   echo slice $snum
-  ${FSLCONVERT} $tmpdir/$tmpnam $tmpdir/${bnm}_slice${snum}.gif
+  ${FSLDIR}/bin/pngappend $tmpdir/${tmpnam}.png $tmpdir/${bnm}_slice${snum}.gif
   n=`echo $n + 1 | bc`;
 done
 
-rm -f $tmpdir/${tmpnam} 
+rm -f $tmpdir/${tmpnam}.png
 
-$FSLDIR/bin/gifmerge -l1000 -35 $tmpdir/${bnm}_slice*.gif > ${volname}_sliceanim.gif
+$FSLDIR/bin/whirlgif -o ${volname}_sliceanim.gif -time 35 -loop 0  $tmpdir/${bnm}_slice*.gif
 
 rm -f $tmpdir/${bnm}_slice*.gif