AFNI program: 3dDetrend

Usage: 3dDetrend [options] dataset
This program removes components from voxel time series using
linear least squares.  Each voxel is treated independently.
The input dataset may have a sub-brick selector string; otherwise,
all sub-bricks will be used.

General Options:
 -prefix pname = Use 'pname' for the output dataset prefix name.
                   [default='detrend']
 -session dir  = Use 'dir' for the output dataset session directory.
                   [default='./'=current working directory]
 -verb         = Print out some verbose output as the program runs.
 -replace      = Instead of subtracting the fit from each voxel,
                   replace the voxel data with the time series fit.
 -normalize    = Normalize each output voxel time series; that is,
                   make the sum-of-squares equal to 1.
           N.B.: This option is only valid if the input dataset is
                   stored as floats!
 -byslice      = Treat each input vector (infra) as describing a set of
                   time series interlaced across slices.  If NZ is the
                   number of slices and NT is the number of time points,
                   then each input vector should have NZ*NT values when
                   this option is used (usually, they only need NT values).
                   The values must be arranged in slice order, then time
                   order, in each vector column, as shown here:
                       f(z=0,t=0)       // first slice, first time
                       f(z=1,t=0)       // second slice, first time
                       ...
                       f(z=NZ-1,t=0)    // last slice, first time
                       f(z=0,t=1)       // first slice, second time
                       f(z=1,t=1)       // second slice, second time
                       ...
                       f(z=NZ-1,t=NT-1) // last slice, last time

Component Options:
These options determine the components that will be removed from
each dataset voxel time series.  They may be repeated to specify
multiple regression.  At least one component must be specified.

 -vector vvv   = Remove components proportional to the columns vectors
                   of the ASCII *.1D file 'vvv'.  You may use a
                   sub-vector selector string to specify which columns
                   to use; otherwise, all columns will be used.
                   For example:
                    -vector 'xyzzy.1D[3,5]'
                   will remove the 4th and 6th columns of file xyzzy.1D
                   from the dataset (sub-vector indexes start at 0).

 -expr eee     = Remove components proportional to the function
                   specified in the expression string 'eee'.
                   Any single letter from a-z may be used as the
                   independent variable in 'eee'.  For example:
                    -expr 'cos(2*PI*t/40)' -expr 'sin(2*PI*t/40)'
                   will remove sine and cosine waves of period 40
                   from the dataset.  Another example:
                    -expr '1' -expr 't' -expr 't*t'
                   will remove a quadratic trend from the data.

 -del ddd      = Use the numerical value 'ddd' for the stepsize
                   in subsequent -expr options.  If no -del option
                   is ever given, then the TR given in the dataset
                   header is used for 'ddd'; if that isn't available,
                   then 'ddd'=1.0 is assumed.  The j-th time point
                   will have independent variable = j * ddd, starting
                   at j=0.  For example:
                     -expr 'sin(x)' -del 2.0 -expr 'z**3'
                   means that the stepsize in 'sin(x)' is delta-x=TR,
                   but the stepsize in 'z**3' is delta-z = 2.

 N.B.: expressions are NOT calculated on a per-slice basis when the
        -byslice option is used.  If you want to do this, you could
        compute vectors with the required time series using 1devel.

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'.