AFNI program: 3dDetrend
Output of -help
Usage: 3dDetrend [options] dataset
* This program removes components from voxel time series using
linear least squares. Each voxel is treated independently.
* Note that least squares detrending is equivalent to orthogonalizing
the input dataset time series with respect to the basis time series
provided by the '-vector', '-polort', et cetera options.
* The input dataset may have a sub-brick selector string; otherwise,
all sub-bricks will be used.
*** You might also want to consider using program 3dBandpass ***
-prefix pname = Use 'pname' for the output dataset prefix name.
-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! (1D files are always 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
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.
will remove the 4th and 6th columns of file xyzzy.1D
from the dataset (sub-vector indexes start at 0).
You can use multiple -vector instances to specify
components from different files.
-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.
-polort ppp = Add Legendre polynomials of order up to and
including 'ppp' in the list of vectors to remove.
-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 have to do this, you could
compute vectors with the required time series using 1deval.
Detrending 1D files
As far as '3d' programs are concerned, you can input a 1D file as
a 'dataset'. Each row is a separate voxel, and each column is a
separate time point. If you want to detrend a single column, then
you need to transpose it on input. For example:
3dDetrend -prefix - -vector G1.1D -polort 3 G5.1D\' | 1dplot -stdin
Note that the '-vector' file is NOT transposed with \', but that
the input dataset file IS transposed. This is because in the first
case the program expects a 1D file, and so knows that the column
direction is time. In the second case, the program expects a 3D
dataset, and when given a 1D file, knows that the row direction is
time -- so it must be transposed. I'm sorry if this is confusing,
but that's the way it is.
NOTE: to have the output file appear so that time is in the column
direction, you'll have to add the option '-DAFNI_1D_TRANOUT=YES'
to the command line, as in
3dDetrend -DAFNI_1D_TRANOUT=YES -prefix - -vector G1.1D -polort 3 G5.1D\' > Q.1D
++ Compile date = May 10 2013
This page auto-generated on
Sat May 11 16:34:42 EDT 2013