Afni3dttest
Afni3dttest is a wrapper for the AFNI (RW Cox, NIH) 3dttest application.
3dttest -- Program to do voxel-by-voxel t-tests on 3D datasets.
AFNI 3dttest was written by Robert Cox, NIH
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 Afni3dttest
This starts up the java interpreter and runs the Afni3dttest
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, 3dttest, please go here.
Afni3dttest window
Information to be entered
- Set 1
This is the list of datasets that you wish to use as the first set.
You may also choose to use the files specified from the design file.
Please see the notes on input datasets to learn more.
- Brick...
- Set 2
This is the list of datasets that you wish to use as the second set.
You may also choose to use the files specified from the design file.
Please see the notes on input datasets to learn more.
- Brick...
- Design file
This is a 2 column text file that contains information about which datasets belong to which set.
To see an example or to find out more, please go to the notes section.
- Compare against constant
Numerical value that will be tested against the mean of the set 2.
- Use paired sample
Perform a paired sample t-test.
- Separate variance estimates
Calculate the variance estimates for the sets seperately.
- Write a dataset containing degrees of freedom
Writes out a seperate dataset with degrees of freedom for each voxel.
This dataset can be used to convert t-values in the output dataset to z-values.
(e.g. 3dcalc -a 'tdif+orig[1]' -b dof+orig -datum float -prefix dof_zz -expr 'fitt_t2z(a,b)'; 3drefit -substatpar 0 fizt dof_zz+orig)
- Set 1 id
This is the text string that will indicate that a dataset belongs in set 1.
- Set 2 id
This is the text string that will indicate that a dataset belongs in set 2.
- Select sets editor
This is a list of programs that may be used to edit the design file on the fly.
- Run sets editor...
This button will start the selected sets editor.
- Set Selector
- Run sets editor... Image name
This is the absolute path of the image.
- Run sets editor... Set
This is the set id to be associated with the image.
- Set Manager
- Prefix
This is the output file prefix.
- Type
Store the output dataset as short or float values
- Session
Write the output dataset to this session directory.
- Workspace size in MB
This is the size of memory that the program will use as a statistical workspace.
- Editing Options...
- Important notes
- Input datasets
3dttest requires that input datasets should be 3d functional datasets with one sub-brick.
It is possible to use datasets with more than one sub-brick with this interface.
If a dataset that has more than one sub-brick, a list will be created containing an entry for each sub-brick.
Please do not enter a multi sub-brick dataset with a sub-brick selection list containing more than one sub-brick
(e.g image+orig[5,7,19]). Only sub-brick selection lists with one sub-brick (e.g image+orig[5]) will work properly.
- Design files
The design files that Afni3dttest uses must be a 2 column ascii file. An example can be seen below.
# example design file
set1 /tmp/image1+orig
set2 /tmp/image2+orig
set2 /tmp/image3+orig
set1 /tmp/image4+orig
In this example the first line is a comment. Any thing to the right of the # symbol is commented out.
The proceeding lines contain two text strings. The first string is the identifier string and the second is absolute path of an image.
The identifier string, which is used to associate the filename with a set, should be identical to one of the strings specified in
the user interface as the set1 or set2 id text strings. Any files with an identifier string which does not match the set1
or set1 id strings will not be used.
Last updated Thu Aug 15 13:25:16 EDT 2002