AFNI program: 3dfim

Program: 3dfim 
Author:  R. W. Cox and B. D. Ward 
Initial Release:  06 Sept 1996 
Latest Revision:  15 August 2001 

 Program:   3dfim 

Purpose:   Calculate functional image from 3d+time data file. 
Usage:     3dfim  [-im1 num]  -input fname  -prefix name 
              -ideal fname  [-ideal fname] [-ort fname] 
 
 options are:
 -im1 num        num   = index of first image to be used in time series 
                         correlation; default is 1  
  
 -input fname    fname = filename of 3d + time data file for input
  
 -prefix name    name  = prefix of filename for saving functional data
  
 -ideal fname    fname = filename of a time series to which the image data
                         is to be correlated. 
  
 -percent p      Calculate percentage change due to the ideal time series 
                 p     = maximum allowed percentage change from baseline 
                         Note: values greater than p are set equal to p. 
  
 -ort fname      fname = filename of a time series to which the image data
                         is to be orthogonalized 
  
             N.B.: It is possible to specify more than
             one ideal time series file. Each one is separately correlated
             with the image time series and the one most highly correlated
             is selected for each pixel.  Multiple ideals are specified
             using more than one '-ideal fname' option, or by using the
             form '-ideal [ fname1 fname2 ... ]' -- this latter method
             allows the use of wildcarded ideal filenames.
             The '[' character that indicates the start of a group of
             ideals can actually be any ONE of these: [{/%
             and the ']' that ends the group can be:  ]}/%
  
             [Format of ideal time series files:
             ASCII; one number per line;
             Same number of lines as images in the time series;
             Value over 33333 --> don't use this image in the analysis]
  
             N.B.: It is also possible to specify more than
             one ort time series file.  The image time series is  
             orthogonalized to each ort time series.  Multiple orts are 
             specified by using more than one '-ort fname' option, 
             or by using the form '-ort [ fname1 fname2 ... ]'.  This 
             latter method allows the use of wildcarded ort filenames.
             The '[' character that indicates the start of a group of
             ideals can actually be any ONE of these: [{/%
             and the ']' that ends the group can be:  ]}/%
  
             [Format of ort time series files:
             ASCII; one number per line;
             At least same number of lines as images in the time series]