3dHist


3dHist computes histograms using functions for generating priors.
If you are not sure you need this particular program, use 3dhistog instead.

Example:
3dHist      -input sigs+orig \n

Options:
   -input DSET: Dset providing values for histogram. Exact 0s are not counted
   -dind SB: Use sub-brick SB from the input rather than 0
   -mask MSET: Provide mask dataset to select subset of input.
   -mask_range BOT TOP: Specify the range of values to consider from MSET.
                        Default is anything non-zero
   -cmask CMASK: Provide cmask expression. Voxels where expression is 0
                 are excluded from computations. For example:
            -cmask '-a T1.div.r+orig -b T1.uni.r+orig -expr step(a/b-10)'
   -thishist HIST.niml.hist: Read this previously created histogram instead
                             of forming one from DSET.
                             Obviously, DSET, or -mask options are not needed
   -prefix PREF: Write histogram to niml file called PREF.niml.hist
   -equalized PREF: Write a histogram equalized version of the input dataset
   Histogram Creation Parameters:
     By default, the program will select bin number, bin width,
     and range automatically. You can also set the parameters manually with
     the following options.
   -nbin K: Use K bins.
   -min MIN: Minimum intensity.
   -max MAX: Maximum intensity.
   -binwidth BW: Bin width
   -ignore_out: Do not count samples outside the user specified range.
   -rhist RHIST.niml.hist: Use previously created histogram to set range
                           and binwidth parameters.

   -showhist: Display histogram to stdout
              You can also graph it with: 1dRplot HistOut.niml.hist

   Histogram Queries:
   -at VAL: Set the value at which you want histogram values
   -get 'PAR1,PAR2,PAR3..': Return the following PAR* properties at VAL
                            Choose from:
                            freq: Frequency (normalized count)
                            count: Count
                            bin: Continuous bin location estimate
                            cdf: Cumulative count
                            rcdf: Reverse cumulative count (from the top)
                            ncdf: The normalized version of cdf
                            nrcdf: The reverse version of ncdf
                            outl: 1.0-(2*smallest tail area)
                               0 means VAL splits area in the middle
                               1 means VAL is at either end of the histogram
                            ALL: All the above.
                   You can select multiple ones with something like:
                        -get 'freq, count, bin'

                   You can also set one of the PAR* to 'upvol' to get
                   the volume (liters) of voxels with values exceeding VAL
                   The use of upvol usually requires option -voxvol too.
  -voxvol VOL_MM3: A voxel's volume in mm^3. To be used with upvol if
                   no dataset is available or if you want to override
                   it.
  -val_at PAR PARVAL: Return the value (magnitude) where histogram property
                      PAR is equal to PARVAL
                      PAR can only be one of: cdf, rcdf, ncdf, nrcdf, upvol
                      For upvol, PARVAL is in Liters
  -quiet: Return a concise output to simplify parsing. For the moment, this
          option only affects output of option -val_at

  Examples:
       #A histogram a la 3dhistog:
       3dHist -input T1+orig.
       #Getting parameters from previously created histogram:
       3dHist -thishist HistOut.niml.hist -at 144.142700
       #Or the reverse query:
       3dHist -thishist HistOut.niml.hist -val_at ncdf 0.132564
       #Compute histogram and find dataset threshold (approximate)
       #such that 1.5 liters of voxels remain above it.
       3dHist -prefix toy -input flair_axial.nii.gz -val_at upvol 1.5



++ Compile date = Sep 27 2020 {AFNI_20.2.19:linux_ubuntu_16_64}