# 3ddelay¶

```
The program estimates the time delay between each voxel time series
in a 3D+time dataset and a reference time series[1][2].
The estimated delays are relative to the reference time series.
For example, a delay of 4 seconds means that the voxel time series
is delayed by 4 seconds with respect to the reference time series.
Usage:
3ddelay
-input fname fname = filename of input 3d+time dataset
DO NOT USE CATENATED timeseries! Time axis is assumed
to be continuous and not evil.
-ideal_file rname rname = input ideal time series file name
The length of the reference time series should be equal to
that of the 3d+time data set.
The reference time series vector is stored in an ascii file.
The programs assumes that there is one value per line and that all
values in the file are part of the reference vector.
PS: Unlike with 3dfim, and FIM in AFNI, values over 33333 are treated
as part of the time series.
-fs fs Sampling frequency in Hz. of data time series (1/TR).
-T Tstim Stimulus period in seconds.
If the stimulus is not periodic, you can set Tstim to 0.
[-prefix bucket] The prefix for the results Brick.
The first subbrick is for Delay.
The second subbrick is for Covariance, which is an
estimate of the power in voxel time series at the
frequencies present in the reference time series.
The third subbrick is for the Cross Correlation
Coefficients between FMRI time series and reference time
series. The fourth subbrick contains estimates of the
Variance of voxel time series.
The default prefix is the prefix of the input dset
with a '.DEL' extension appended to it.
[-polort order] Detrend input time series with polynomial of order
'order'. If you use -1 for order then the program will
suggest an order for you (about 1 for each 150 seconds)
The minimum recommended is 1. The default is -1 for auto
selection. This is the same as option Nort in the plugin
version.
[-nodtrnd] Equivalent to polort 0, whereby only the mean is removed.
NOTE: Regardless of these detrending options, No detrending is
done to the reference time series.
[-uS/-uD/-uR] Units for delay estimates. (Seconds/Degrees/Radians)
You can't use Degrees or Radians as units unless
you specify a value for Tstim > 0.
[-phzwrp] Delay (or phase) wrap.
This switch maps delays from:
(Seconds) 0->T/2 to 0->T/2 and T/2->T to -T/2->0
(Degrees) 0->180 to 0->180 and 180->360 to -180->0
(Radians) 0->pi to 0->pi and pi->2pi to -pi->0
You can't use this option unless you specify a
value for Tstim > 0.
[-nophzwrp] Do not wrap phase (default).
[-phzreverse] Reverse phase such that phase -> (T-phase)
[-phzscale SC] Scale phase: phase -> phase*SC (default no scaling)
[-bias] Do not correct for the bias in the estimates [1][2]
[-nobias | -correct_bias] Do correct for the bias in the estimates
(default).
[-dsamp] Correct for slice timing differences (default).
[-nodsamp ] Do not correct for slice timing differences .
[-mask mname] mname = filename of 3d mask dataset
only voxels with non-zero values in the mask would be
considered.
[-nfirst fnum] fnum = number of first dataset image to use in
the delay estimate. (default = 0)
[-nlast lnum] lnum = number of last dataset image to use in
the delay estimate. (default = last)
[-co CCT] Cross Correlation Coefficient threshold value.
This is only used to limit the ascii output (see below).
[-asc [out]] Write the results to an ascii file for voxels with
[-ascts [out]] cross correlation coefficients larger than CCT.
If 'out' is not specified, a default name similar
to the default output prefix is used.
-asc, only files 'out' and 'out.log' are written to disk
(see ahead)
-ascts, an additional file, 'out.ts', is written to disk
(see ahead)
There a 9 columns in 'out' which hold the following
values:
1- Voxel Index (VI) : Each voxel in an AFNI brick has a
unique index.
Indices map directly to XYZ coordinates.
See AFNI plugin documentations for more info.
2..4- Voxel coordinates (X Y Z): Those are the voxel
slice coordinates. You can see these coordinates
in the upper left side of the AFNI window.
To do so, you must first switch the voxel
coordinate units from mm to slice coordinates.
Define Datamode -> Misc -> Voxel Coords ?
PS: The coords that show up in the graph window
may be different from those in the upper left
side of AFNI's main window.
5- Duff : A value of no interest to you. It is preserved
for backward compatibility.
6- Delay (Del) : The estimated voxel delay.
7- Covariance (Cov) : Covariance estimate.
8- Cross Correlation Coefficient (xCorCoef) :
Cross Correlation Coefficient.
9- Variance (VTS) : Variance of voxel's time series.
The file 'out' can be used as an input to two plugins:
'4Ddump' and '3D+t Extract'
The log file 'out.log' contains all parameter settings
used for generating the output brick.
It also holds any warnings generated by the plugin.
Some warnings, such as 'null time series ...' , or
'Could not find zero crossing ...' are harmless. '
I might remove them in future versions.
A line (L) in the file 'out.ts' contains the time series
of the voxel whose results are written on line (L) in the
file 'out'.
The time series written to 'out.ts' do not contain the
ignored samples, they are detrended and have zero mean.
Random Comments/Advice:
The longer you time series, the better. It is generally recomended that
the largest delay be less than N/10, N being time series' length.
The algorithm does go all the way to N/2.
If you have/find questions/comments/bugs about the plugin,
send me an E-mail: saadz@mail.nih.gov
Ziad Saad Dec 8 00.
[1] : Bendat, J. S. (1985). The Hilbert transform and applications
to correlation measurements, Bruel and Kjaer Instruments Inc.
[2] : Bendat, J. S. and G. A. Piersol (1986). Random Data analysis and
measurement procedures, John Wiley & Sons.
Author's publications on delay estimation using the Hilbert Transform:
[3] : Saad, Z.S., et al., Analysis and use of FMRI response delays.
Hum Brain Mapp, 2001. 13(2): p. 74-93.
[4] : Saad, Z.S., E.A. DeYoe, and K.M. Ropella, Estimation of FMRI
Response Delays. Neuroimage, 2003. 18(2): p. 494-504.
++ Compile date = Aug 10 2020 {AFNI_20.2.11:linux_ubuntu_16_64}
```