Afni3dTqual

Afni3dTqual is a wrapper for the AFNI (RW Cox, NIH) waver application.
It computes a quality index for each sub-brick in a 3D+time dataset. The results are written to stdout.
RWCox - Aug 2001
For more information about the AFNI package, see the AFNI Homepage

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

Invocation

java  Afni3dTqual

Afni3dTqual window

Information to be entered

• Input Dataset
  Use the file browser button to choose the input dataset.
• Print range with each quality index
  Print the median-3.5*MAD and median+3.5*MAD values out with each quality index, so they can be plotted.
• Save results
  Specify filename and location to save the results of 3dtqual.
• View results
  View a graph of the output of Afni3dTqual.
• Quality Index
  Choose one of the following:
  • Spearman
    Quality index is 1 minus the rank correlation coefficient of each sub-brick with the median sub-brick.
  • Quadrant
    Quality index is 1 minus the quadrant correlation coefficient as the quality index.
• No clipping
  Default; do not use any clipping options.
• Clip off values below here
  Clip off values below the specified number in the median sub-brick. Mutually exclusive with automatic clipping.
• Perform automatic clipping
  Clip off low-intensity regions in the median sub-brick.This prevents a large number of nearly 0 voxels outside the brain from biasing the calculations.

• Menubar
• Toolbar
• Output window