Performing the Uniformity Correction

The Uniformity Correction tool takes a single input image, estimates the bias field, and creates an new image with the non-uniformity corrected. The new image can either be saved to disk, or loaded into Jim depending on your selection:

Load the result or save the result to disk

The estimated bias field can also be saved as an image on disk and applied to other images of the same dimensions.

There is just one settings that affects the quality of the correction:

Setting the number of levels-of-detail for bias field correction

Setting a higher number of levels-of-detail will result in a more detailed estimate of the bias field.

  • Setting a value which is too low will result in not enough detail in the bias field estimate to model the true bias field. The bias field estimate will be too smooth to capture the details of the true bias field.
  • Setting a value which is too high will cause bias field estimation to take much longer, and will result in spurious detail in the bias field estimate. Then some of the intensity variation which is due to true variations in tissue type will be removed, reducing the image contrast. If you create an image of the bias field, by selecting the the Saving the bias field image to disk check-box, the resulting bias field image will start to show variations which follow the type of tissue if the number of levels-of-detail is set to high.
Level-of-detail=1 Level-of-detail=3 Level-of-detail=5
Bias field with the level-of-detail=1 Bias field with the level-of-detail=3 Bias field with the level-of-detail=5
Not high enough to capture
the bias field. 		  Too high - grey/white matter
variations are being corrected.

A setting of 3 should be about right for most MR images.

You may also need to set the maximum number of iterations. Uniformity correction is an iterative procedure, and the maximum number of iterations allowed is set in the text box: Setting the maximum number of iterations for bias field correction. In the unlikely event that the uniformity correction procedure fails with a message that the maximum number of iterations was exceeded, you should increase the value from its default.

Select the image you want to correct by clicking on the Open an image file icon, or by typing in the folder (directory) and file name of the image, or by pressing the right mouse button and selecting from the menu of recently-used images.

Selecting the image to be bias corrected

Now click on the button to do the uniformity bias correction button to perform the correction. If you have chosen to save the corrected image to disk, then a File Chooser will pop up, prompting you to choose a file name for the new image. Otherwise, the result will be loaded into Jim.

Input Image Masking

The standard masking options are available to exclude pixels in the calculation of the bias. This can be useful for removing portions of the image where bias correction is not important.