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
-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 histogramALL: 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