AFNI program: 3dpc

Principal Component Analysis of 3D Datasets
Usage: 3dpc [options] dataset dataset ...

Each input dataset may have a sub-brick selector list.
Otherwise, all sub-bricks from a dataset will be used.

OPTIONS:
  -dmean        = remove the mean from each input brick (across space)
  -vmean        = remove the mean from each input voxel (across bricks)
                    [N.B.: -dmean and -vmean are mutually exclusive]
                    [default: don't remove either mean]
  -vnorm        = L2 normalize each input voxel time series
                    [occurs after the de-mean operations above,]
                    [and before the brick normalization below. ]
  -normalize    = L2 normalize each input brick (after mean subtraction)
                    [default: don't normalize]
  -pcsave sss   = 'sss' is the number of components to save in the output;
                    it can't be more than the number of input bricks
                    [default = all of them = number of input bricks]
  -prefix pname = Name for output dataset (will be a bucket type);
                    also, the eigen-timeseries will be in 'pname'.1D
                    (all of them) and in 'pnameNN.1D' for eigenvalue
                    #NN individually (NN=00 .. 'sss'-1, corresponding
                    to the brick index in the output dataset)
                    [default value of pname = 'pc']
  -1ddum ddd    = Add 'ddd' dummy lines to the top of each *.1D file.
                    These lines will have the value 999999, and can
                    be used to align the files appropriately.
                    [default value of ddd = 0]
  -verbose      = Print progress reports during the computations
  -float        = Save eigen-bricks as floats
                    [default = shorts, scaled so that |max|=10000]
  -mask mset    = Use the 0 sub-brick of dataset 'mset' as a mask
                    to indicate which voxels to analyze (a sub-brick
                    selector is allowed) [default = use all voxels]

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'.