++ 3ddelay: AFNI version=AFNI_2011_12_21_1014 (Dec 16 2015) [64-bit] ++ Authored by: Ziad Saad (with help from B Douglas Ward) 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
-fs fs Sampling frequency in Hz. of data time series (1/TR).
[-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]
[-dsamp] Correct for slice timing differences (default).
[-nodsamp ] Do not correct for slice timing differences .
[-asc [out]] Write the results to an ascii file for voxels with
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 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.
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.
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.
++ Compile date = Dec 16 2015