3dLocalHistog


Usage: 3dLocalHistog [options] dataset ...

This program computes, at each voxel, a count of how many times each
unique value occurs in a neighbhood of that voxel, across all the input
datasets.
 * The neighborhood is defined by the '-nbhd' option.
 * The input datasets should be in short or byte format, without
   scaling factors attached.
 * You can input float format datasets, but the values will be rounded
   to an integer between -32767 and 32767 before being used.
 * You can also output the overall histogram of the dataset collection,
   via the '-hsave' option (as a 1D file).  This is simply the count of how
   many times each value occurs.
 * For histograms of continuously valued datasets see program 3dLocalstat
   with option -stat hist*

OPTIONS
-------
 -nbhd 'nnn'   = The string 'nnn' defines the region around each
                 voxel that will be extracted for the statistics
                 calculation.  The format of the 'nnn' string is
                 the same as in 3dLocalstat:
                 * 'SPHERE(r)'
                 * 'RECT(a,b,c)'
                 * 'RHDD(a)'
                 * 'TOHD(a)'
                 * If no '-nbhd' option is given, then just the voxel
                   itself is used -- in which case, the input dataset(s)
                   must comprise a total of at least 2 sub-bricks!

 -prefix ppp   = Use string 'ppp' as the prefix for the output dataset.

 -hsave sss    = Save the overall histogram into file 'sss'.  This file will
                 have 2 columns:   value  count
                 Values with zero count will not be shown in this file.

 -lab_file LL  = Use file 'LL' as a label file.  The first column contains
                 the numbers, the second column the corresponding labels.
                 * You can use a column selector to choose the columns you
                   want.  For example, if the first column has the labels
                   and the second the values, use 'filename[1,0]'.

 -exclude a..b = Exclude values from 'a' to 'b' from the counting.
                 * Zero (0) will never be excluded.
                 * You can use '-exclude' more than once.
 -excNONLAB    = If '-lab_file' is used, then exclude all values that are NOT
                 in the label file (except for 0, of course).
 -mincount mm  = Exclude values which appear in the overall histogram
                 fewer than 'mm' times.
                 * Excluded  values will be treated as if they are zero
                   (and so appear in the '0:Other' output sub-brick).
                 * The overall histogram output by '-hsave' is NOT altered
                   by the use of '-mincount' or '-exclude' or '-excNONLAB'.

 -prob         = Normally, the output dataset is a set of counts.  This
                 option converts each count to a 'probability' by dividing
                 by the total number of counts at each voxel.
                 * The resulting dataset is stored as bytes, in units of
                   0.01, so that p=1 corresponds to 1/0.01=100.

 -quiet        = Stop the highly informative progress reports.

OUTPUT DATASET
--------------
 * For each distinct value a sub-brick is produced.
 * The zero value will be first; after that, the values will appear in
   increasing order.
 * If '-lab_file' is used, then the sub-brick label for a given value's count
   will be of the form 'value:label'; for example, '2013:rh.lingual'.
 * For values NOT in the '-lab_file', the label will just be of the form 'value:'.
 * For the first (value=0) sub-brick, the label will be '0:Other'.

Author: RWCox - April 2013

++ Compile date = Jan 21 2020 {AFNI_20.0.01:linux_ubuntu_16_64}