AFNI program: 3dfim+
Output of -help
++ 3dfim+: AFNI version=AFNI_2011_12_21_1014 (May 31 2013) [64-bit]
++ Authored by: B. Douglas Ward
Program to calculate the cross-correlation of an ideal reference waveform
with the measured FMRI time series for each voxel.
-input fname fname = filename of input 3d+time dataset
[-input1D dname] dname = filename of single (fMRI) .1D time series
[-mask mname] mname = filename of 3d mask dataset
[-nfirst fnum] fnum = number of first dataset image to use in
the cross-correlation procedure. (default = 0)
[-nlast lnum] lnum = number of last dataset image to use in
the cross-correlation procedure. (default = last)
[-polort pnum] pnum = degree of polynomial corresponding to the
baseline model (pnum = 0, 1, etc.)
(default: pnum = 1). Use -1 for no baseline model.
[-fim_thr p] p = fim internal mask threshold value (0 <= p <= 1)
to get rid of low intensity voxels.
(default: p = 0.0999), set p = 0.0 for no masking.
[-cdisp cval] Write (to screen) results for those voxels
whose correlation stat. > cval (0 <= cval <= 1)
[-ort_file sname] sname = input ort time series file name
-ideal_file rname rname = input ideal time series file name
Note: The -ort_file and -ideal_file commands may be used
more than once.
Note: If files sname or rname contain multiple columns,
then ALL columns will be used as ort or ideal
time series. However, individual columns or
a subset of columns may be selected using a file
name specification like 'fred.1D[0,3,5]', which
indicates that only columns #0, #3, and #5 will
be used for input.
[-out param] Flag to output the specified parameter, where
the string 'param' may be any one of the following:
Fit Coef L.S. fit coefficient for Best Ideal
Best Index Index number for Best Ideal (count starts at 1)
% Change P-P amplitude of signal response / Baseline
Baseline Average of baseline model response
Correlation Best Ideal product-moment correlation coefficient
% From Ave P-P amplitude of signal response / Average
Average Baseline + average of signal response
% From Top P-P amplitude of signal response / Topline
Topline Baseline + P-P amplitude of signal response
Sigma Resid Std. Dev. of residuals from best fit
All This specifies all of the above parameters
Spearman CC Spearman correlation coefficient
Quadrant CC Quadrant correlation coefficient
Note: Multiple '-out' commands may be used.
Note: If a parameter name contains imbedded spaces, the
entire parameter name must be enclosed by quotes,
e.g., -out 'Fit Coef'
[-bucket bprefix] Create one AFNI 'bucket' dataset containing the
parameters of interest, as specified by the above
The output 'bucket' dataset is written to a file
with the prefix name bprefix.
++ Compile date = May 31 2013
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Mon Jun 3 08:37:24 EDT 2013