Afni3dfim
Afni3dfim is a wrapper for the AFNI (RW Cox, NIH) 3dfim application.
3dfim -- Implements the "correlation method" on a 3D+time series.
AFNI 3dfim was written by 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 Afni3dfim
This starts up the java interpreter and runs the Afni3dfim 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.
Afni3dfim window
There isn't much to document here. The widgets behavior is consistant with
that of all FisWidgets and functions accordingly.
Information to be entered
- Input dataset
The input dataset is where you put your Afni 3d+time file. The file
can be either the header (.HEAD) or the brick (.BRIK) so long as the file
is in the format filename+orig.BRIK. All Afni files should have a +orig
after their filename, but in case the format changes or this is merely
a convention that might go out of date, you will have to rename your files
so they have the +orig.BRIK or +orig.HEAD extension.
- Output prefix
Your output prefix is not a file, hence, you don't need a browse button.
The prefix is inputted by the user and then is used to replace the filename
of the output. For example, a 3d+time file is called alpha+orig, and given
the prefix omega. The output file will be omega+orig. You cannot select
your output directory. It is automatically the same as the one where you
are getting input from.
- Ideal Correlation
Ideal correlation takes a text file containing one ASCII number on
the line relating to the correlation. Refer to the 3dfim documentation.
This program does not check to ensure that you have one number per every
voxel in the data set.
- ort time series
This program can also use a time seris to which the image data is to
be othogonalized. The format is similar to that used by the Ideal Correlation
field.
- Percent Intensity
Percent Intensity change be changed with this value. The default is
100% of the intensity of the original image. However, you can modify that
by clicking and entering a whole number value between 1 and 100
- Index Number
The Index Number tells you with what number of image in the data set
you want to start your analysis on.
Last updated Fri Dec 01 17:41:58 EST 2000