Processing Options

Having set up the Brain Atrophy tool's input images as detailed in the Introduction, you can now set up the other processing options:

Brain Atrophy tool options

  • Selecting whether to skip pre-processing - skull stripping and registering the FLAIR to the the T1-weighted imput images. Select this option only if your T1-weighted input images are already skull-stripped, and the T1-weighted and FLAIR images are already co-registered (aligned). If selected, these pre-processing steps are skipped.

  • Selecting whether to provide extra regularisation when diffeomorphically registering the template image to the T1-weighted imput images. When selected, this tells Jim to apply extra regularisation when diffeomorphically registering the template image to the T1-weighted input images. If the registration of the prior probability images results in severe local distortions, then it is worth trying to do the registration with extra regularisation to smooth out the irregularities.

  • The Markov Random Field regularisation strength slider. This sets the strength of the Markov Random Field regularisation, which suppresses transitions in tissue between adjacent pixels during the segmentation. Selecting a higher value will lead to more uniform class probabilities, at the expense of being able to capture true changes in tissue class for small regions. You should normally not need to change the setting from its default value of 5.

  • A checkbox to indicate that lesions are to be segmented. Select if you want to segment brain lesions that are hyperintense on the FLAIR images. This checkbox will only appear if you have 2 input image contrasts (T1-weighted and FLAIR), since both image contrasts are needed for lesion segmentation.

    When selected, the Lesion probability threshold slider will become visible:

    Slider to set the lesion probability threshold

    The output of the lesion segmentation is a lesion probability map. This is then contoured at a probability threshold to produce ROIs that outline the lesions. Setting a higher threshold will result in smaller lesions; a lower threshold gives larger lesion ROIs. A setting of 0.5 should be close to optimal for most images.

Finally, set the base name for the output images:

Setting the output images base name for the Brain Atrophy tool

In this example, we have set the file name "Test" in the home folder.

Several intermediate output images will be created in the selected folder. These are:

  • Prior probability images. These are the template prior probability images, registered to the (co-registered) input T1-weighted images, for the GM, WM, CSF and lateral ventricles.
  • If you have more than one time-point, images of the Jacobian determinants will be created: an image for every pair of successive time-points. If, for example, you have set a base name of "Test", and there are two time-points, then an image called Test_Det_1_2 will be produced, which shows the Jacobian determinants for the deformation from the first time-point to the second.
  • If you have more than one time-point, and are performing lesion segmentation, an image of the intensity difference in the FLAIR images for every pair of successive time-points will be created. If, for example, you have set a base name of "Test", there are two time-points, then an image called Test_D1_2 will be produced, which shows the change in intensity from the first time-point to the second. This is useful for identifying new and resolved lesions across time-points.

Clicking the Button to start the atrophy analysis button will start the analysis. However, see these sections for additional guidance on the steps needed for different types of analysis: