# 3dNLfim¶

```
This program calculates a nonlinear regression for each voxel of the
input AFNI 3d+time data set. The nonlinear regression is calculated
by means of a least squares fit to the signal plus noise models which
are specified by the user.
Usage with terminal options:
3dNLfim
-help show this help
-help_models show model help from any that have it
(can come via AFNI_MODEL_HELP_ALL)
One can get help for an individual model, *if* it exists, by
setting a similar environment variable, and providing some
non-trivial function option (like -load_models), e.g.,
3dNLfim -DAFNI_MODEL_HELP_CONV_PRF_6=Y -load_models
Indifidual help should be available for any model with help
via -help_models.
-load_models simply load all models and exit
(this is for testing or getting model help)
General usage:
3dNLfim
-input fname fname = filename of 3d + time data file for input
[-mask mset] Use the 0 sub-brick of dataset 'mset' as a mask
to indicate which voxels to analyze (a sub-brick
selector is allowed) [default = use all voxels]
[-ignore num] num = skip this number of initial images in the
time series for regresion analysis; default = 0
****N.B.: default ignore value changed from 3 to 0,
on 04 Nov 2008 (BHO day).
[-inTR] set delt = TR of the input 3d+time dataset
[The default is to compute with delt = 1.0 ]
[The model functions are calculated using a
time grid of: 0, delt, 2*delt, 3*delt, ... ]
[-TR delt] directly set the TR of the time series model;
can be useful if the input file is a .1D file
(transposed with the \' operator)
[-time fname] fname = ASCII file containing each time point
in the time series. Defaults to even spacing
given by TR (this option overrides -inTR).
-signal slabel slabel = name of (non-linear) signal model
-noise nlabel nlabel = name of (linear) noise model
-sconstr k c d constraints for kth signal parameter:
c <= gs[k] <= d
**N.B.: It is important to set the parameter
constraints with care!
**N.B.: -sconstr and -nconstr options must appear
AFTER -signal and -noise on the command line
-nconstr k c d constraints for kth noise parameter:
c+b[k] <= gn[k] <= d+b[k]
[-nabs] use absolute constraints for noise parameters:
c <= gn[k] <= d [default=relative, as above]
[-nrand n] n = number of random test points [default=19999]
[-nbest b] b = use b best test points to start [default=9]
[-rmsmin r] r = minimum rms error to reject reduced model
[-fdisp fval] display (to screen) results for those voxels
whose f-statistic is > fval [default=999.0]
[-progress ival] display (to screen) results for those voxels
every ival number of voxels
[-voxel_count] display (to screen) the current voxel index
--- These options choose the least-square minimization algorithm ---
[-SIMPLEX] use Nelder-Mead simplex method [default]
[-POWELL] use Powell's NEWUOA method instead of the
Nelder-Mead simplex method to find the
nonlinear least-squares solution
[slower; usually more accurate, but not always!]
[-BOTH] use both Powell's and Nelder-Mead method
[slowest, but should be most accurate]
--- These options generate individual AFNI 2 sub-brick datasets ---
--- [All these options must be AFTER options -signal and -noise]---
[-freg fname] perform f-test for significance of the regression;
output 'fift' is written to prefix filename fname
[-frsqr fname] calculate R^2 (coef. of multiple determination);
store along with f-test for regression;
output 'fift' is written to prefix filename fname
[-fsmax fname] estimate signed maximum of signal; store along
with f-test for regression; output 'fift' is
written to prefix filename fname
[-ftmax fname] estimate time of signed maximum; store along
with f-test for regression; output 'fift' is
written to prefix filename fname
[-fpsmax fname] calculate (signed) maximum percentage change of
signal from baseline; output 'fift' is
written to prefix filename fname
[-farea fname] calculate area between signal and baseline; store
with f-test for regression; output 'fift' is
written to prefix filename fname
[-fparea fname] percentage area of signal relative to baseline;
store with f-test for regression; output 'fift'
is written to prefix filename fname
[-fscoef k fname] estimate kth signal parameter gs[k]; store along
with f-test for regression; output 'fift' is
written to prefix filename fname
[-fncoef k fname] estimate kth noise parameter gn[k]; store along
with f-test for regression; output 'fift' is
written to prefix filename fname
[-tscoef k fname] perform t-test for significance of the kth signal
parameter gs[k]; output 'fitt' is written
to prefix filename fname
[-tncoef k fname] perform t-test for significance of the kth noise
parameter gn[k]; output 'fitt' is written
to prefix filename fname
--- These options generate one AFNI 'bucket' type dataset ---
[-bucket n prefixname] create one AFNI 'bucket' dataset containing
n sub-bricks; n=0 creates default output;
output 'bucket' is written to prefixname
The mth sub-brick will contain:
[-brick m scoef k label] kth signal parameter regression coefficient
[-brick m ncoef k label] kth noise parameter regression coefficient
[-brick m tmax label] time at max. abs. value of signal
[-brick m smax label] signed max. value of signal
[-brick m psmax label] signed max. value of signal as percent
above baseline level
[-brick m area label] area between signal and baseline
[-brick m parea label] signed area between signal and baseline
as percent of baseline area
[-brick m tscoef k label] t-stat for kth signal parameter coefficient
[-brick m tncoef k label] t-stat for kth noise parameter coefficient
[-brick m resid label] std. dev. of the full model fit residuals
[-brick m rsqr label] R^2 (coefficient of multiple determination)
[-brick m fstat label] F-stat for significance of the regression
[-noFDR] Don't write the FDR (q vs. threshold)
curves into the output dataset.
(Same as 'setenv AFNI_AUTOMATIC_FDR NO')
--- These options write time series fit for ---
--- each voxel to an AFNI 3d+time dataset ---
[-sfit fname] fname = prefix for output 3d+time signal model fit
[-snfit fname] fname = prefix for output 3d+time signal+noise fit
-jobs J Run the program with 'J' jobs (sub-processes).
On a multi-CPU machine, this can speed the
program up considerably. On a single CPU
machine, using this option is silly.
J should be a number from 1 up to the
number of CPU sharing memory on the system.
J=1 is normal (single process) operation.
The maximum allowed value of J is 32.
* For more information on parallelizing, see
https://afni.nimh.nih.gov/afni/doc/misc/parallize.html
* Use -mask to get more speed; cf. 3dAutomask.
----------------------------------------------------------------------
Signal Models (see the appropriate model_*.c file for exact details) :
Null : No Signal
(no parameters)
see model_null.c
SineWave_AP : Sinusoidal Response
(amplitude, phase)
see model_sinewave_ap.c
SquareWave_AP : Square Wave Response
(amplitude, phase)
see model_squarewave_ap.c
TrnglWave_AP : Triangular Wave Response
(amplitude, phase)
see model_trnglwave_ap.c
SineWave_APF : Sinusoidal Wave Response
(amplitude, phase, frequency)
see model_sinewave_apf.c
SquareWave_APF : Sinusoidal Wave Response
(amplitude, phase, frequency)
see model_squarewave_apf.c
TrnglWave_APF : Sinusoidal Wave Response
(amplitude, phase, frequency)
see model_trnglwave_apf.c
Exp : Exponential Function
(a,b): a * exp(b * t)
see model_exp.c
DiffExp : Differential-Exponential Drug Response
(t0, k, alpha1, alpha2)
see model_diffexp.c
GammaVar : Gamma-Variate Function Drug Response
(t0, k, r, b)
see model_gammavar.c
Beta : Beta Distribution Model
(t0, tf, k, alpha, beta)
see model_beta.c
* The following convolved functions are generally convolved with
the time series in AFNI_CONVMODEL_REF, allowing one to specify
multiple event onsets, varying durations and varying resopnse
magnitudes.
ConvGamma : Gamma Vairate Response Model
(t0, amp, r, b)
see model_convgamma.c
ConvGamma2a : Gamma Convolution with 2 Input Time Series
(t0, r, b)
see model_convgamma2a.c
ConvDiffGam : Difference of 2 Gamma Variates
(A0, T0, E0, D0, A1, T1, E1, D1)
see model_conv_diffgamma.c
for help : setenv AFNI_MODEL_HELP_CONVDIFFGAM YES
3dNLfim -signal ConvDiffGam
demri_3 : Dynamic (contrast) Enhanced MRI
(K_trans, Ve, k_ep)
see model_demri_3.c
for help : setenv AFNI_MODEL_HELP_DEMRI_3 YES
3dNLfim -signal demri_3
ADC : Diffusion Signal Model
(So, D)
see model_diffusion.c
michaelis_menton : Michaelis/Menten Concentration Model
(v, vmax, k12, k21, mag)
see model_michaelis_menton.c
Expr2 : generic (3dcalc-like) expression with
exactly 2 'free' parameters and using
symbol 't' as the time variable;
see model_expr2.c for details.
ConvCosine4 : 4-piece Cosine Convolution Model
(A, C1, C2, M1, M2, M3, M4)
see model_conv_cosine4.c
for help : setenv AFNI_MODEL_HELP_CONV_COSINE4 YES
3dNLfim -signal ConvCosine4
Conv_PRF : 4-param Population Receptive Field Model
(A, X, Y, sigma)
see model_conv_PRF.c
for help : setenv AFNI_MODEL_HELP_CONV_PRF YES
3dNLfim -signal bunnies
Conv_PRF_6 : 6-param Population Receptive Field Model
(A, X, Y, sigma, sigrat, theta)
see model_conv_PRF_6.c
for help : setenv AFNI_MODEL_HELP_CONV_PRF_6 YES
3dNLfim -signal bunnies
Conv_PRF_DOG : 6-param 'Difference of Gaussians' PRF Model
(as Conv_PRF, but with second A and sigma)
(A, X, Y, sig, A2, sig2)
see model_conv_PRF_DOG.c
for help : setenv AFNI_MODEL_HELP_CONV_PRF_DOG YES
3dNLfim -signal bunnies
----------------------------------------
Noise Models (see the appropriate model_*.c file for exact details) :
Zero : Zero Noise Model
(no parameters)
see model_zero.c
Constant : Constant Noise Model
(constant)
see model_constant.c
Linear : Linear Noise Model
(constant, linear)
see model_linear.c
Linear+Ort : Linear+Ort Noise Model
(constant, linear, Ort)
see model_linplusort.c
Quadratic : Quadratic Noise Model
(constant, linear, quadratic)
see model_quadratic.c
++ Compile date = Aug 10 2020 {AFNI_20.2.11:linux_ubuntu_16_64}
```