AFNI program: 3dhistog
Output of -help
++ 3dhistog: AFNI version=AFNI_24.3.08 (Dec 6 2024) [64-bit]
Compute histogram of 3D Dataset
Usage: 3dhistog [editing options] [histogram options] dataset
The editing options are the same as in 3dmerge
(i.e., the options starting with '-1').
The histogram options are:
-nbin # Means to use '#' bins [default=100]
-dind i Means to take data from sub-brick #i, rather than #0
-omit x Means to omit the value 'x' from the count;
-omit can be used more than once to skip multiple values.
-mask m Means to use dataset 'm' to determine which voxels to use
-roi_mask r Means to create a histogram for each non-zero value in
dataset 'r'. If -mask option is also used, dataset 'r' is
masked by 'm' before creating the histograms.
-doall Means to include all sub-bricks in the calculation;
otherwise, only sub-brick #0 (or that from -dind) is used.
-noempty Only output bins that are not empty.
This does not apply to NIML output via -prefix.
-notitle Means to leave the title line off the output.
-log10 Output log10() of the counts, instead of the count values.
This option cannot be used with -pdf or with -prefix
-pdf Output the counts divided by the number of samples.
This option is only valid with -prefix
-min x Means specify minimum (inclusive) of histogram.
-max x Means specify maximum (inclusive) of histogram.
-igfac Means to ignore sub-brick scale factors and histogram-ize
the 'raw' data in each volume.
Output options for integer and floating point data
By default, the program will determine if the data is integer or float
even if the data is stored as shorts with a scale factor.
Integer data will be binned by default to be 100 or the maximum number of
integers in the range, whichever is less. For example, data with the range
(0..20) gives 21 bins for each integer, and non-integral bin boundaries
will be raised to the next integer (2.3 will be changed to 3, for instance).
If the number of bins is higher than the number of integers in the range,
the bins will be labeled with floating point values, and multiple bins
may be zero between the integer values
Float data will be binned by default to 100 bins with absolute limits for
the min and max if these are specified as inclusive. For example,
float data ranging from (0.0 to 20.0) will be binned into bins that
are 0.2 large (0..0.199999, 0.2..0.399999,...,19.8..20.0)
To have bins divided at 1.0 instead, specify the number of bins as 20
Bin 0 is 0..0.9999, Bin 1 is 1.0 to 1.9999, ..., Bin 20 is 19 to 20.0000
giving a slight bias to the last bin
-int Treat data and output as integers
-float Treat data and output as floats
-unq U.1D Writes out the sorted unique values to file U.1D.
This option is not allowed for float data
If you have a problem with this, write
Ziad S. Saad (saadz@mail.nih.gov)
-prefix HOUT: Write a copy of the histogram into file HOUT.1D
you can plot the file with:
1dplot -hist -sepscl -x HOUT.1D'[0]' HOUT.1D'[1,2]'
or
1dRplot -input HOUT.1D
Without -prefix, the histogram is written to stdout.
Use redirection '>' if you want to save it to a file.
The format is a title line, then three numbers printed per line:
bottom-of-interval count-in-interval cumulative-count
There is no 1dhistog program, for the simple reason that you can use
this program for the same purpose, as in this example:
3dhistog -nbin 50 -notitle -min 0 -max .01 err.1D > ehist.1D
1dplot -hist -x ehist.1D'[0]' -xlabel 'err.1D' -ylabel 'histo' ehist.1D'[1]'
-- by RW Cox, V Roopchansingh, and ZS Saad
INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
'r1+orig[3..5]' {sub-brick selector}
'r1+orig<100..200>' {sub-range selector}
'r1+orig[3..5]<100..200>' {both selectors}
'3dcalc( -a r1+orig -b r2+orig -expr 0.5*(a+b) )' {calculation}
For the gruesome details, see the output of 'afni -help'.
++ Compile date = Dec 6 2024 {AFNI_24.3.08:linux_ubuntu_24_64}
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