# 3dDetrend¶

```
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 ***
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! (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
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).
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 = Aug 10 2020 {AFNI_20.2.11:linux_ubuntu_16_64}
```