AfniAlphaSim
AfniAlphaSim is a wrapper for the AFNI (RW Cox, NIH) AlphaSim application.
3dFWHM -- Simulates noise-only 3D+time series and activation detection therefrom, in order to estimate the probability of false positives. Used when analytical estimates for this p-value are unavailable.
AFNI AlphaSim 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 AfniAlphaSim
This starts up the java interpreter and runs the AfniAlphaSim application.
You need to have set up your environment
for javain order for this to work.
For information on how to invoke the command line program, AlphaSim, please go here.
AfniAlphaSim window
Information to be entered
- Image size in voxels (x, y, z)
This is the dimensions of the 3d image in voxels along the x, y, and z axes.
- Voxel size in mm (x, y, z)
This is the dimensions of a voxel in millimeters along the x, y and z axes.
- Mask file
The given 3d dataset is used as a mask to indicate which voxels to include in the cluster information.
Note that the dimensions of the mask file will use in place of the values above.
- Find probaility of true detection
Calculate the probability of detection of a user specified activation region.
- Active region in voxels (x, y, z)
This is the dimensions of the true activation region.
- Separation in z-scores
This is used to specify the setparation, in standard z-scores,
between the mean of the siganl distribution and the mean of the noise distribution.
- FWHM (all axes)
This is the width of the Gaussian filter which is applied to each axis of the randomly generated image to simulate spatial correlation of voxel intensites.
- FWHM (x, y, z)
This is the widths of the Gaussian filters to be applied to each axis of the image independently.
- Sigma (all axes)
This is the standard deviation of the Gaussian filter which is applied to each axis of the randomly generated image to simulate spatial correlation of voxel intensites.
- Sigma (x, y, z)
This is the standard deviations of the Gaussian filters to be applied to each axis of the image independently.
- Cluster connection radius in mm
This value is the cluster connctivity radius.
That is, two activated voxels whose centers are separated by a distance less
than the radius are assumed to be members of the same cluster.
- Threshold probability
This value is used to set the individual voxel probability threshold.
- Monte Carlo iterations
This value is use to set the number of Monte Carlo iterations to be performed.
- Verbose
Enable verbose output during operation.
- Output file
Write the output to this file. Otherwise, the output is written to the output window.
Last updated Thu Sep 13 10:50:19 EDT 2001