AFNI program: 3dExtrema

Program:          3dExtrema 
Author:           B. Douglas Ward 
Initial Release:  12 April 2001 
Latest Revision:  15 August 2001 

This program finds local extrema (minima or maxima) of the input       
dataset values for each sub-brick of the input dataset.  The extrema   
may be determined either for each volume, or for each individual slice.
Only those voxels whose corresponding intensity value is greater than  
the user specified data threshold will be considered.                  

Usage: 3dExtrema  options  datasets                                  
where the options are:                                                 
-prefix pname    = Use 'pname' for the output dataset prefix name.     
  OR                 [default = NONE; only screen output]              
-output pname                                                          
                                                                       
-session dir     = Use 'dir' for the output dataset session directory. 
                     [default='./'=current working directory]          
                                                                       
-quiet           = Flag to suppress screen output                      
                                                                       
-mask_file mname = Use mask statistic from file mname.                 
                   Note: If file mname contains more than 1 sub-brick, 
                   the mask sub-brick must be specified!               
-mask_thr m        Only voxels whose mask statistic is greater         
                   than m in abolute value will be considered.         
                                                                       
-data_thr d        Only voxels whose value (intensity) is greater      
                   than d in abolute value will be considered.         
                                                                       
-sep_dist d        Min. separation distance [mm] for distinct extrema  
                                                                       
Choose type of extrema (one and only one choice):                      
-minima            Find local minima.                                  
-maxima            Find local maxima.                                  
                                                                       
Choose form of binary relation (one and only one choice):              
-strict            >  for maxima,  <  for minima                       
-partial           >= for maxima,  <= for minima                       
                                                                       
Choose boundary criteria (one and only one choice):                    
-interior          Extrema must be interior points (not on boundary)   
-closure           Extrema may be boudary points                       
                                                                       
Choose domain for finding extrema (one and only one choice):           
-slice             Each slice is considered separately                 
-volume            The volume is considered as a whole                 
                                                                       
Choose option for merging of extrema (one and only one choice):        
-remove            Remove all but strongest of neighboring extrema     
-average           Replace neighboring extrema by average              
-weight            Replace neighboring extrema by weighted average     
                                                                       
Command line arguments after the above are taken to be input datasets. 


INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
  'r1+orig[3..5]'                                    {sub-brick selector}
  'r1+orig<100.200>'                                 {sub-range selector}
  'r1+orig[3..5]<100..200>'                          {both selectors}
  '3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )'  {calculation}
For the gruesome details, see the output of 'afni -help'.