3dTfilter takes as input a dataset, filters the time series in
each voxel as ordered by the user, and outputs a new dataset.
The data in each voxel is processed separately.

The user (you?) specifies the filter functions to apply.
They are applied in the order given on the command line:
  -filter rank -filter adaptive:7
means to do the following operations
  (1) turn the data into ranks
  (2) apply the adaptive mean filter to the ranks

** This program is a work in progress, and more capabilities
   will be added as time allows, as the need arises, and as
   the author's whims bubble to the surface of his febrile brain.

** This program is for people who have Sisu.


 -input inputdataset

 -prefix outputdataset

 -filter FunctionName
     At least one '-filter' option is required!
     The FunctionName values that you can give are:

        rank       = smallest value is replaced by 0,
                     next smallest value by 1, and so forth.
                     ** This filter is pretty useless.

        adaptive:H = adaptive mean filter with half-width of
                     'H' time points (H > 0).
                     ** At most one 'adaptive' filter can be used!
                     ** The filter 'footprint' is 2*H+1 points.
                     ** This filter does local smoothing over the
                        'footprint', with values far away from
                        the local median being weighted less.

        adetrend:H = apply adaptive mean filter with half-width
                     of 'H' time points to get a local baseline,
                     then subtract this baseline from the actual
                     data, to provide an adaptive detrending.
                     ** At most one 'adaptive' OR 'adetrend' filter
                        can be used.

        despike    = apply the 'NEW25' despiking algorithm, as in
                     program 3dDespike.

        despike:H  = apply the despiking algorithm over a window
                     of half-with 'H' time points (667 > H > 3).
                     ** H=12 is the same as 'despike'.
                     ** At most one 'despike' filter can be used.

        detrend:P  = (least squares) detrend with polynomials of up
                     order 'P' for P=0, 1, 2, ....
                     ** At most one 'detrend' filter can be used!
                     ** You can use both '-adetrend' and '-detrend',
                        but I don't know why you would try this.

 3dTfilter -input fred.nii -prefix fred.af.nii -filter adaptive:7

Author: The Programmer with No Name