NISNORM(1)                       NIS 3.4                September 8, 2000

NAME
     nisnorm - image mean normalization 

SYNOPSIS
     nisnorm [-azvh] [-s stem] [-m mean] [-t threshold] [-d outdir] [-f filelist] [inputfile]

DESCRIPTION
     nisnorm performs mean normalization on a set of neuroimaging
     scans.  Each image in the set is normalized to a reference image 
     (assumed to be the first image in the set), such that the mean 
     signal intensity in the image is equivalent.  Normalization can be 
     specified to be either additive or multiplicative (scaled).

     Input to nisnorm is a list of file names specifying the
     scans to be normalized.  The list is read from the standard input
     or can be redirected from a text file.

OPTIONS

     -a   performs additive normalization, rather than multiplicative 
          (which is the default).
     
     -z   compresses input files after reading.

     -h   show usage.

     -m mean
          normalize all images to the specified mean intensity.  If this
          flag is not specified, all images will be normalized to the mean
          intensity of the first image.

     -s stem
          uses stem as output file prefix, rather than prepending an 'n' to
          the input image name.

     -t threshold
          calculates mean based only on voxels whose mean signal intensity is 
          above threshold.  Provides a means of ignoring background pixels.

     -v   verbose output to stdout; pipes cannot be used with this option.

     -d outdir
          output directory (will use current working directory if not given).

     -f filelist
          file with filenames to be normed (optional; will read from
          standard input if not given).

     ARGUMENTS:
     inputfile
          input image filename (optional; will read from standard input
          if not included).


LIMITS AND DIAGNOSTICS
     At most 40000 image files are allowed.