AfniViewer

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  AfniViewer 

AfniViewer window

Information to be entered

• Session directory
  This is the directory that contains the datasets you wish to read in.
• New window title
  This text will be used as the new title in the AFNI windows.
• Gamma correction
  This value is the gamma correction factor for your monitor.
• Available colors
  This the maximum number of colors you what AFNI to use.
• Quiet startup
  AFNI will suppress verbose start up messages when selected.
• Show Xt warnings
  Enable AFNI to show Xt warning messages.
• View flipped images
  Have AFNI display images in 'flipped' radioogy convention (left on right).
• More Options...
  These are options which are used infrequently
  • More Options... Use image options
    Allow AFNI to read in a series of 2D images as a dataset. However, most of the advanced featues will not be avaliable.
  • More Options... Use dataset options
    Have AFNI read in the datasets given.
  • More Options... Images to read
    This is the list of 2D images to read in.
  • More Options... 3d dataset
    Interperet the series of images as a single 3D dataset.
  • More Options... 3d+ dataset, one slice in time
    Interperet the series of images as a single slice over a period of time.
  • More Options... 3d+ dataset, t-axis first with N points in time
    Interperet the series of images as a 3d dataset over time, with a given number of time points
  • More Options... 3d+ dataset, z-axis first with N slices in space
    Interperet the series of images as a 3d dataset over time, with a given number of slices per volume
  • More Options... Ratio of y to x
    This is the downscreen pixel size times the across-screen (x) pixel dimension.
  • More Options... Convert data to
    Convert the imput images to the one of the following types: byte, short, float, or complex
  • More Options... Ratio of z to x
    This is the slice thickness times the across-screen (x) pixel dimension.
  • More Options... Resize images to fit the first one
    This tells AFNI that all images should be resized to fit the first one. By default, images must be the same size or afni will stop.
  • More Options... Datasets to read
    This is the list of datasets to read in
  • More Options... Read layout file
    This is a file that describes the window layout to use.
  • More Options... Recursively search for more session directories
    This will make AFNI search for more session directories within other session directories
  • More Options... Maximum level of recursion
    AFNI will search for mored directories unless it reaches this depth.
  • More Options... Purge data to disk
    AFNI will conserve memory by purging data to disk.
  • More Options... Pbar uses only positive values
    The color 'pbar' will use only positive function values
  • More Options... Ignore 1D files
    AFNI will not to read *.1D timeseries files from the session directories. The *.1D files in the directories listed in the AFNI_TSPATH environment variable will still be read (if this variable is not set, then './' will be scanned for *.1D files.)
  • More Options... No quality checks for transformations
    Disable any quality checks for transformations to ACPC or Talairach
  • More Options... Disable plugins
    Have AFNI not use any plugins.
  • More Options... Unique colors for each controller window
    AFNI will create a unique set of colors for each AFNI controller window. This allows different datasets to be viewed with different grayscales or colorscales. Note that -unique will only work on displays that support 12 bit PseudoColor (e.g., SGI workstations) or TrueColor.
  • More Options... Ignore afnirc files
    Allow AFNI to ignore any .afnirc files in your home directory
  • More Options... Ignore first N time points
    AFNI will ignore this many time points from the beginning of a dataset.
  • More Options... Talariach brick size
    This is the brick size used for Talairach datasets. The possible sizes are big and small.
  • More Options... Enable plugouts
    This will make AFNI do one of the following: Listen for plugouts, Listen for plugouts and print out lots of messages, Don't to plugouts
  • Orientation
• Version
  Print the version of AFNI and do nothing else.

• Menubar
• Toolbar
• Output window