7.1.95. 3dLocalHistog

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++ 3dLocalHistog: AFNI version=AFNI_2011_12_21_1014 (Dec 16 2015) [64-bit] ++ Authored by: Thorin Oakenshield 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 = Dec 16 2015

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