Afni3dfimPlus

Afni3dfimPlus is a wrapper for the AFNI (RW Cox, NIH) 3dfim+ application.
3dfim+ -- Implements the "correlation method" on a 3D+time series, with many additional output options.
AFNI 3dfim+ was written by B. Douglas Ward, Medical College of Wisconsin.
For more information about the AFNI package, see the AFNI Homepage

To see the AFNI postscript documentation please go here.

To read the help documentation generated from the command line go here.

To learn about afni data types follow this link.

Invocation

java Afni3dfimPlus

This starts up the java interpreter and runs the Afni3dfimPlus application. You need to have set up your environment for java in order for this to work.

For information on how to invoke the command line program, 3dfim+, please go here.

Afni3dfimPlus window

Information to be entered

Input dataset
This is the filename of the 3d+ dataset that will be analyzed.
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.
Ideal file
This is the name of the file that represents an "ideal" time series function.
Select columns from multi-column file
Treat the ideal file as a multi-column time series file.
Select ideal columns...
Click this to bring up select ideal columns

Select ideal columns... Variable name
This is the name given for each column.
Select ideal columns... Include
This specifies if the the variable should be used.

Use ort file
When selected, this file that will be used to orthogonalize an "ideal" time series function.
Select columns from multi-column file
Treat the ort file as a multi-column time series file.
Select ort columns...
Click this to bring up select ideal columns

Select ort columns... Variable name
This is the name of given for each column.
Select ort columns... Include
This specifies if the the variable should be used.

Options...
Click this to bring up options

Options... Run 1 voxel only
When selected, this time series file will be used instead of 3d+ dataset. Options that would otherwise generate output files are ignored.
Options... Use mask file
Use this 3d dataset as a mask.
Options... Set image range
Set the range of images to be used in the calcuations.
Options... first
This is the where the first image used is located.
Brick...
Options... last
This is the where the last image used is located.
Brick...
Options... Baseline polynomial order
This is the degree of the polynomial use in the baseline model.
Options... Internal mask threshold
Use this value to set a threshold for an internal mask. Any voxel whose intensity is less than threshold * average is excluded from the analysis.
Options... Display correlation coefficients over
Enable the screen to display information for each voxel where the absolute value of the correlation coefficient is of greater than or equal value.

Select Statistics...
Click this to bring up select statistics

Select Statistics... Fit Coef
Calculate the least squares fit coeffcient for Best Index.
Select Statistics... Best Index
Calculate the index number for best ideal.
Select Statistics... % Change
Calculate 100 * P - P amplitude of signal response / Baseline.
Select Statistics... Baseline
Calculate the average of baseline response.
Select Statistics... Correlation
Calculate the product-moment correlation coefficient for Best Index.
Select Statistics... % From Ave
Calculate 100 * P - P amplitude of signal response / Average.
Select Statistics... Average
Calculate baseline + average of signal response.
Select Statistics... % From Top
Calculate 100 * P - P amplitude of signal response / Topline.
Select Statistics... Topline
Calculate baseline + P - P amplitiude of signal response
Select Statistics... Sigma Resid
Find standard deviation of residuals from best fit.
Select Statistics... All
Calculate all of the above statistics.
Select Statistics... Spearman CC
Calculate the Spearman correlation coefficient.
Select Statistics... Quadrant CC
Calculate the Quadrant correlation coefficient.

Last updated Wed Sep 12 17:26:18 EDT 2001