Afni3dAnova

Afni3dAnova is a wrapper for the AFNI (RW Cox, NIH) 3dANOVA, 3dANOVA2, and 3dANOVA3 applications.
3dANOVA, 3dANOVA2, and 3dANOVA3 -- This series of program performs 1-way, 2-way, and 3-way ANOVA tests across a collection of 3D datasets, on a voxel-by-voxel basis.
The AFNI 3dANOVA, 3dANOVA2, and 3dANOVA3 programs 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 Afni3dAnova

This starts up the java interpreter and runs the Afni3dAnova 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, 3dANOVA, please go here.

For information on how to invoke the command line program, 3dANOVA2, please go here.

For information on how to invoke the command line program, 3dANOVA3, please go here.

Afni3dAnova window

Information to be entered

Use design file only
When selected, the filenames contained in the design file will be used. Please see the notes on design files to learn more.
Image dataset(s)
One or more datasets can be specified by one with the Browse and Brick buttons.
Image directory
All of the datasets in the given directory will be used.
Image filelist
All of the datasets listed in this text file will be used.
Brick...
Design file
This is a multi-column file that contains design levels and the corresponding datasets. Each column contains levels for a single factor. The last column is assumed to hold the cooresponding dataset filenames. That column is not used when using a filelist, directory, or dataset list as input.
Design editor...
This is an interface to create and edit design files.
Use test prefixes
Each test that is performed will be written to a seperate dataset with the given prefix.
Write to a single output bucket
Each test will be a sub-brick of a functional bucket dataset with the given prefix.
Model
This is a list of all possible ANOVA models available.
Means...
For each panel except the last, the mean of level i for a factor is calculated. The final panel will calculate the mean of the cell at level i of factor A, level j of factor B, etc. Note that some tabs and column may not be used because of the number of factors and the type of ANOVA model.
Differences...
For each panel except the last, the difference of the mean at level i and the mean at level j for a factor is calculated. The final panel will calculate the difference of the mean of the cell at level i of factor A, level j of factor B, etc. and the mean of the cell at level k of factor A, level l of factor B, etc. Note that some tabs and column may not be used because of the number of factors and the type of ANOVA model.
F Tests...
These are the available f-test from all of the ANOVA programs.
- F Tests... Treatment
  Calculate an F-test for the treatment effect.
- F Tests... A Main
  Calculate an F-test for equality of level means for factor A.
- F Tests... B Main
  Calculate an F-test for equality of level means for factor B.
- F Tests... C Main
  Calculate an F-test for equality of level means for factor C.
- F Tests... AB Interaction
  Calculate an F-test for interaction effect of factors A and B.
- F Tests... AC Interaction
  Calculate an F-test for interaction effect of factors A and C.
- F Tests... BC Interaction
  Calculate an F-test for interaction effect of factors B and C.
- F Tests... ABC Interaction
  Calculate an F-test for interaction effect of factors A, B, and C.
Contrasts...
For each panel except the last, the contrast of level i for a factor is calculated. The final panel will calculate the contrast of cell means of all factors. Note that some tabs and column may not be used because of the number of factors and the type of ANOVA model.
Display single voxel
If checked, the intermediate ANOVA calculations for a single voxel are displayed. Note that the input value is an index in the array of voxels that compose a sub-brick of a dataset.

Important notes

Design files
The design files that Afni3dAnova uses must be a multi column ascii file. An example can be seen below.
TAP T1 /tmp/image1+orig TAP T2 /tmp/image2+orig TAP T3 /tmp/image3+orig TAP T4 /tmp/image4+orig NO_TAP T1 /tmp/image5+orig NO_TAP T2 /tmp/image6+orig NO_TAP T3 /tmp/image7+orig NO_TAP T4 /tmp/image8+orig
Each column in the file, except the last, represents a factor. A maximum of 3 factors is allowed by Afni3dAnova. The last column is a list of absolute paths to datasets to be used by the program. Each line in the file contains an absolute path to a dataset and a series of text strings for each factor. These text strings are a way represent the level for each factor that the dataset belongs to. For example, the line TAP T4 /tmp/image4+orig states that the dataset /tmp/image4+orig is in the level represented by the string TAP in the first factor and the level represented by the string T4 in the second factor.

Last updated Wed Jul 17 17:47:08 EDT 2002