Afni3dcalc

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 Afni3dcalc

For information on how to invoke the command line program, 3dcalc, please go here.

Afni3dcalc window

Information to be entered

• 3dcalc variables...
  The 3d calc variables button will pop up another window when clicked. This window is where you specify all your variables needed in your expression.
• 3dcalc variables... File
  The File box will list the path of the file you selected by using the variable specifier below.
• 3dcalc variables... File
  This is where one specifies a file. One can either enter a pathname in the textfield, or click the "Browse" button next to it to select a .BRIK or .HEAD file.
• Brick...
• 3dcalc variables... Variable
  This field cannot be changed by the user. It will display what variable name a file will be assigned when the "Add Variable" button is clicked.
• Output Prefix
  Files tend to go by a structure of "Afni+orig.HEAD". The prefix you specify here will replace the Afni part of the file name. It will be outputted to the user's current working directory unless the Output Directory option is used.
• Output Directory
  Specify a directory to write out the dataset. Clicking the Browse button to its right lets you select which directory that is.
• Expression
  This is the field where you enter in your expression. Please look at the postscript documentation for a list of valid expressions, see link above.
• Output Data Type
  This is where specify any output coercion. The file outputted by Afni3dcalc will be converted to this data type you specify unless default is selected. Then the output type is that of the first input file, variable A.
• Verbose
  Enable verbose output mode.
• fscale
  Implement fscaling in Afni3dcalc. Please refer to the original Afni3dcalc documentation for more information.
• gscale
  Implement gscaling, which is similar to fscaling, but will force all sub-bricks to have the same scale factor. It is very useful for 3d+time datasets. For more information, refer to the original 3dcalc documentation.
• nscale
  Implement no scaling to output byte or short datasets. This is useful when operating on mask datasets whose output is 0's and 1's. For more information, refer to the original 3dcalc documentation.
• History parent
  The history of the dataset that is represented by this variable will be used to create the history of the output dataset.
• TR
  This value will be used as the TR for the output dataset.
• Create time axis
  Force the creation of a 3d+time dataset when only 3d datasets are used as input. The output dataset will have the time axis of the length specified in the GUI.
• with time step
  This value will be used as the time step of the generated output dataset. The time step may be expressed as seconds or milliseconds. Please note that user has the option of using the TR option to set the time step.
• Adjust RGB scale
  Change how 3dcalc reads in RGB valued datasets. 3dcalc uses the following formula to find a value for a single RGB voxel

  value = A*r + B*g + C*b, where A = 0.299, B = 0.587, and C = 0.114.

  There is a field for each color so the values of A, B, and C can be adjusted according to the user's needs.

• Menubar
• Toolbar
• Output window