Preset Calculations

Jim Image Algebra has several built-in formulae to serve as examples, and to perform some of the more common operations. You can set up Image Algebra to perform one of these calculations by selecting one of the items in the Presets menu:

algebra_presets

At the time of writing, there are currently nine preset functions:

  • Add images. Adds two (or more) input images.
  • Subtract images. Subtracts two input images.
  • Magnetisation transfer ratio (MTR) (1% bins). This uses two input images, with variable names M0 and Ms to calculate the MTR. Pixel intensities in the calculated MTR image will be between 0 and 100, with 100 steps giving a 1% bin size.
  • Magnetisation transfer ratio (MTR) (0.1% bins). As above, but pixel intensities in the calculated MTR image will be between 0 and 1000, with 1000 steps giving a 0.1% bin size.
  • T2 estimation from a double-echo T2-weighted MRI sequence. Substitute the two echo times TE1 and TE2 in the formula for the echo times applying to your pair of input images.
  • R2 estimation from a double-echo T2-weighted MRI sequence. Substitute the two echo times TE1 and TE2 in the formula for the echo times applying to your pair of input images.
  • M0 estimation (pixel intensity at zero echo time) from a double-echo T2-weighted MRI sequence. Substitute the two echo times TE1 and TE2 in the formula for the echo times applying to your pair of input images.
  • Apparent diffusion coefficient (ADC) estimation from non-diffusion-weighted (T2-weighted) and diffusion-weighted images. Substitute the b-factor into the formula. The variable names are T2 and DW for the T2-weighted and diffusion-weighted images respectively.
  • Mean diffusivity estimation from a non-diffusion-weighted (T2-weighted) and 3 diffusion-weighted images with weighting in each of three orthogonal directions. Substitute the b-factor into the formula. The variable names are T2, DW1, DW2, and DW3 for the T2-weighted and three diffusion-weighted images respectively.

If you have suggestions for more formulae to include in the Presets menu, please mail them to support.

Creating Your Own Presets

If you find yourself repeatedly performing calculations on images using the Algebra tool, and typing in the formula etc., you can save the whole set-up as a preset. Simply set up the Algebra tool as you want, then choose Save As Preset ... from the Presets menu. You will be prompted to give your new Preset a title:

preset_title

Enter some text that describes your new Preset; this text will appear as a new Preset in the in the Presets menu.

To remove a preset from the menu, click on Manage Presets ..., and select the Preset you want to remove.