fixed help text

fslstats.cc

@@ -21,7 +21,7 @@ bool uthr_used=false;
 
 void print_usage(const string& progname) {
   cout << "Usage: fslstats <input> [options]" << endl << endl;
-  cout << endl;
+  cout << "Note - options are applied in order, e.g. -M -l 10 -M will report the non-zero mean, apply a threshold and then report the new nonzero mean" << endl << endl;
   cout << "-l <lthresh> : set lower threshold" << endl;
   cout << "-u <uthresh> : set upper threshold" << endl;
   cout << "-r           : output <robust min intensity> <robust max intensity>" << endl;
@@ -45,8 +45,7 @@ void print_usage(const string& progname) {
   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; 
-  cout << 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 << endl;
   cout << "Note - thresholds are not inclusive ie lthresh<allowed<uthresh" << endl;
 }