7.1.87. 3dHistΒΆ

Link to classic view

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 = Dec 16 2015

Table Of Contents

This Page