7.1.108. 3dNLfimΒΆ

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++ 3dNLfim: AFNI version=AFNI_2011_12_21_1014 (Dec 16 2015) [64-bit] ++ Authored by: B. Douglas Ward 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: 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.
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
ConvGamma2a : Gamma Convolution with 2 Input Time Series
(t0, r, b) see model_convgamma2a.c
ConvGamma : Gamma Vairate Response Model
(t0, amp, r, b) see model_convgamma.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
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 = Dec 16 2015

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