Task-Based Help - Lesion Volumes using the Contouring Method

In this first example, we will measure the total volume of white-matter lesions in a patient with multiple sclerosis using the contouring method. In this disease, the areas of damaged brain white matter appear hyperintense on a PD or T₂-weighted MR image.

1. First you need to load you image into Jim. Either load the image directly or use the image importer to load an image.
2. Next you will need to outline the lesions on each slice of the image. Select a central slice of the image by double-clicking on it, and set single image layout by pressing the button. Adjust the contrast using the sliders. Set the contrast for all slices to this setting using the Link button. Now zoom and scroll the image so that you can see the lesions in more detail. Set the zoom and scroll the same for all slices by pressing the button. Enlarge the Jim frame if you wish by dragging the corners of the frame.
3. Open the ROI Toolkit. Using the contouring function attempt to outline the lesions automatically by clicking on their edge. If this fails, either edit the contoured outlines or draw the outlines manually.
4. Step through the slices using the paging buttons, and outline all the lesions on all the slices.
5. When you have all the lesions outlined, calculate the volume of lesions that you have outlined. The totaliser will sum up the areas and multiply by the slice thickness to give you the total lesion volume. The totaliser also allows you to write the total to a disk file as a permanent record of the computed volume.
   Note: If the image was acquired with an inter-slice gap, the computed volume should be corrected by multiplying the volume by:

   (slice-thickness + inter-slice-gap) / slice-thickness.

6. Save your ROIs to disk as a permanent record of your definition of the lesions.
7. You are now ready to progress to the next scan to be measured. Proceed from step 1.