:orphan: .. _ahelp_3dROIstats: ********** 3dROIstats ********** .. contents:: :local: | .. code-block:: none 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 -nzvolume Compute the volume 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 = Mar 24 2024 {AFNI_24.0.17:linux_ubuntu_16_64}