3dfim+

Program to calculate the cross-correlation of an ideal reference waveform
with the measured FMRI time series for each voxel.

Usage:
3dfim+
-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)
                     (default: disabled)
[-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
                   '-out' commands.
                   The output 'bucket' dataset is written to a file
                   with the prefix name bprefix.

++ Compile date = Oct 13 2022 {AFNI_22.3.03:linux_ubuntu_16_64}