# 3dPolyfit¶

## Usage: 3dPolyfit [options] dataset¶

```
* Fits a polynomial in space to the input dataset and outputs that fitted dataset.
* You can also add your own basis datasets to the fitting mix, using the
'-base' option.
* You can get the fit coefficients using the '-1Dcoef' option.
```

## Options:¶

```
-nord n = Maximum polynomial order (0..9) [default order=3]
[n=0 is the constant 1]
[n=-1 means only use volumes from '-base']
-blur f = Gaussian blur input dataset (inside mask) with FWHM='f' (mm)
-mrad r = Radius (voxels) of preliminary median filter of input
[default is no blurring of either type; you can]
[do both types (Gaussian and median), but why??]
[N.B.: median blur is slower than Gaussian]
-prefix pp = Use 'pp' for prefix of output dataset (the fit).
[default prefix is 'Polyfit'; use NULL to skip this output]
-resid rr = Use 'rr' for the prefix of the residual dataset.
[default is not to output residuals]
-1Dcoef cc = Save coefficients of fit into text file cc.1D.
[default is not to save these coefficients]
-automask = Create a mask (a la 3dAutomask)
-mask mset = Create a mask from nonzero voxels in 'mset'.
[default is not to use a mask, which is probably a bad idea]
-mone = Scale the mean value of the fit (inside the mask) to 1.
[probably this option is not useful for anything]
-mclip = Clip fit values outside the rectilinear box containing the
mask to the edge of that box, to avoid weird artifacts.
-meth mm = Set 'mm' to 2 for least squares fit;
set it to 1 for L1 fit [default method=2]
[Note that L1 fitting is slower than L2 fitting!]
-base bb = In addition to the polynomial fit, also use
the volumes in dataset 'bb' as extra basis functions.
[If you use a base dataset, then you can set nord]
[to -1, to skip using any spatial polynomial fit.]
-verb = Print fun and useful progress reports :-)
```

## Notes:¶

```
* Output dataset is always stored in float format.
* If the input dataset has more than 1 sub-brick, only sub-brick #0
is processed. To fit more than one volume, you'll have to use a script
to loop over the input sub-bricks, and then glue (3dTcat) the results
together to get a final result. A simple example:
#!/bin/tcsh
set base = model.nii
set dset = errts.nii
set nval = `3dnvals $dset`
@ vtop = $nval - 1
foreach vv ( `count 0 $vtop` )
3dPolyfit -base "$base" -nord 0 -mask "$base" -1Dcoef QQ.$vv -prefix QQ.$vv.nii $dset"[$vv]"
end
3dTcat -prefix QQall.nii QQ.0*.nii
1dcat QQ.0*.1D > QQall.1D
m QQ.0*
exit 0
* If the '-base' dataset has multiple sub-bricks, all of them are used.
* You can use the '-base' option more than once, if desired or needed.
* The original motivation for this program was to fit a spatial model
to a field map MRI, but that didn't turn out to be useful. Nevertheless,
I make this program available to someone who might find it beguiling.
* If you really want, I could allow you to put sign constraints on the
fit coefficients (e.g., say that the coefficient for a given base volume
should be non-negative). But you'll have to beg for this.
-- Emitted by RWCox
++ Compile date = Jan 21 2020 {AFNI_20.0.01:linux_ubuntu_16_64}
```