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]’
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
-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 ‘>’.
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 16 2015