AFNI program: 3dLocalHistog
Output of -help
++ 3dLocalHistog: AFNI version=AFNI_24.3.06 (Oct 31 2024) [64-bit]
++ Authored by: Bilbo Baggins
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 = Oct 31 2024 {AFNI_24.3.06:linux_ubuntu_24_64}
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