Afni3dTshift
Afni3dTshift is a wrapper for the AFNI (RW Cox, NIH) 3dTshift application.
3dTshift -- Utility program to time-shift voxel time series to the same temporal origin.
AFNI 3dTshift was written by Robert W. Cox, Medical College of Wisconsin.
For more information about the AFNI package, see the AFNI Homepage
Currently, there is no postscript documentation for this program. Please
read the help documentation here
for more information.
To read the help documentation generated from the command line go here.
To learn about afni data types follow this link.
Invocation
java Afni3dTshift
This starts up the java interpreter and runs the Afni3dTshift application.
You need to have set up your environment
for java in order for this to work.
Afni3dTshift window
Information to be entered
- Input dataset
This is the input dataset to be shifted to a new temporal origin.
This program accepts datasets that are modified on input according
to the following schemes:
'r1+orig[3..5]'{sub-brick selector}
The sub-range selector <> and 3dcalc schemes are supported by the
command line program, but not in the GUI.
- Output prefix
The general form of the dataset filenames is "prefix+view.NAME" and
the text typed in will replace the "prefix" section of the output filename.
Note that this program will fail if you specfify a prefix that is already
used by another file in the same directory.
- Interpolation Method
This is where you specify the interpolation method to use. The following
are the possible selections:
- FourierUse a Fourier method (the default, most accurate & slowest)
- heptic Use a heptic (7th order) Lagrange polynomial interpolation
- quintic Use a quintic (5th order) Lagrange polynomial interpolation
- cubic Use a cubic (3rd order) Lagrange polynomial interpolation
- linear Use a linear (1st order) Lagrange polynomial interpolation (least accurate)
- Verbose
This checkbox will enable verbose output when checked.
- Advanced Options...
Click this to bring up advanced options
- Advanced Options... Override header TR
When selected, this value will be used as the length of time it took
to acquire one image. The units may be selected on the right of the text
field. You may use milliseconds(ms, the default), seconds(s), or Hertz(Hz)
- Advanced Options... Mean & linear
If you wish to add the mean and linear trends back to the output after
shifting, select this.
- Advanced Options... Mean only
If you wish to add the mean trend only to the output after shifting,
select this.
- Advanced Options... None
If you wish to add the neither the mean or linear trend, select this.
- Advanced Options... Use average slice time
Select this to use the average slice time as the offset to align the
slices in the dataset (default option).
- Advanced Options... Align slices to time offset
Select this to enter an offset to align all of the slices in the dataset.
Note: The program will fail if an offset is not between the minimum and
maximum slice temporal offsets inclusively.
- Advanced Options... Align all slices to this slice
Select this to use the time offset of a slice to align all others in
the dataset. Note: The slice should be between 0 and the number of slices
- 1.
- Advanced Options... Use pattern in header
Select this to use the temporal pattern in the header to read in temporal
offsets (default option).
- Advanced Options... Temporal pattern file
Select this to use a file that describes the temporal pattern to use.
- Advanced Options... Temporal pattern
Select this to use a pattern from the drop-down box. The choices are
as follows:
- alternating, +z alternating in the positive z direction
- alternating, -z alternating in the negative z direction
- sequential, +z sequential in the posititve z direction
- sequential, -z sequential in the negative z direction
- Multiple Run Options
Last updated Wed Sep 12 15:40:34 EDT 2001