# 3dROIstats¶

```
Usage: 3dROIstats -mask[n] mset [options] datasets
Display statistics over masked regions. The default statistic
is the mean.
There will be one line of output for every sub-brick of every
input dataset. Across each line will be every statistic for
every mask value. For instance, if there 3 mask values (1,2,3),
then the columns Mean_1, Mean_2 and Mean_3 will refer to the
means across each mask value, respectively. If 4 statistics are
requested, then there will be 12 stats displayed on each line
(4 for each mask region), besides the file and sub-brick number.
Examples:
3dROIstats -mask mask+orig. 'func_slim+orig[1,3,5]'
3dROIstats -minmax -sigma -mask mask+orig. 'func_slim+orig[1,3,5]'
Options:
-mask[n] mset Means to use the dataset 'mset' as a mask:
If n is present, it specifies which sub-brick
in mset to use a la 3dcalc. Note: do not include
the brackets if specifying a sub-brick, they are
there to indicate that they are optional. If not
present, 0 is assumed
Voxels with the same nonzero values in 'mset'
will be statisticized from 'dataset'. This will
be repeated for all the different values in mset.
I.e. all of the 1s in mset are one ROI, as are all
of the 2s, etc.
Note that the mask dataset and the input dataset
must have the same number of voxels and that mset
must be BYTE or SHORT (i.e., float masks won't work
without the -mask_f2short option).
-mask_f2short Tells the program to convert a float mask to short
integers, by simple rounding. This option is needed
when the mask dataset is a 1D file, for instance
(since 1D files are read as floats).
Be careful with this, it may not be appropriate to do!
-numROI n Forces the assumption that the mask dataset's ROIs are
denoted by 1 to n inclusive. Normally, the program
figures out the ROIs on its own. This option is
useful if a) you are certain that the mask dataset
has no values outside the range [0 n], b) there may
be some ROIs missing between [1 n] in the mask data-
set and c) you want those columns in the output any-
way so the output lines up with the output from other
invocations of 3dROIstats. Confused? Then don't use
this option!
-zerofill ZF For ROI labels not found, use 'ZF' instead of a blank
in the output file. This option is useless without -numROI.
The option -zerofill defaults to '0'.
-roisel SEL.1D Only considers ROIs denoted by values found in SEL.1D
Note that the order of the ROIs as specified in SEL.1D
is not preserved. So an SEL.1D of '2 8 20' produces the
same output as '8 20 2'
-debug Print out debugging information
-quiet Do not print out labels for columns or rows
-nomeanout Do not print out the mean column. Default is
to always start with the mean value.
This option cannot be used with -summary
-longnames Prints the entire name of the sub-bricks
-nobriklab Do not print the sub-brick label next to its index
-1Dformat Output results in a 1D format that includes
commented labels
-1DRformat Output results in a 1D format that includes
uncommented labels. This format does not work well with
typical 1D programs, but it is useful for R functions.
The following options specify what stats are computed. By default
the mean is always computed.
-nzmean Compute the mean using only non_zero voxels. Implies
the opposite for the normal mean computed
-nzsum Compute the sum using only non_zero voxels.
-nzvoxels Compute the number of non_zero voxels
-minmax Compute the min/max of all voxels
-nzminmax Compute the min/max of non_zero voxels
-sigma Compute the standard deviation of all voxels
-nzsigma Compute the standard deviation of all non_zero voxels
-median Compute the median of all voxels.
-nzmedian Compute the median of non_zero voxels.
-summary Only output a summary line with the grand mean
across all briks in the input dataset.
This option cannot be used with -nomeanout.
-mode Compute the mode of all voxels. (integral valued sets only)
-nzmode Compute the mode of non_zero voxels.
-pcxyz Compute the principal direction of the voxels in the ROI
including the three eigen values. You'll get 12 values out
per ROI, per sub-brick, with this option.
pc0x pc0y pc0z pc1x pc1y pc1z pc2x pc2y pc2z eig0 eig1 eig2
-nzpcxyz Same as -pcxyz, but exclude zero valued voxels.
-pcxyz+ Same as -pcxyz, but also with FA, MD, Cl, Cp, and Cs computed
from the three eigen values.
You will get 17 values out per ROI, per sub-brick, beginning
with all the values from -pcxyz and -nzpcxyz then followed by
FA MD Cl Cp Cs
-nzpcxyz+ Same as -nzpcxyz, but also with FA, MD, Cl, Cp, and Cs.
-key Output the integer key for the ROI in question
The output is printed to stdout (the terminal), and can be
saved to a file using the usual redirection operation '>'.
N.B.: The input datasets and the mask dataset can use sub-brick
selectors, as detailed in the output of 3dcalc -help.
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 = Jan 27 2020 {AFNI_20.0.03:linux_ubuntu_16_64}
```