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.
- First you need to load you image into Jim. Either
load the image directly or use the
image importer to load an image.
- 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.
- 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.
- Step through the slices using the paging buttons, and outline all the
lesions on all the slices.
- 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
.
- Save your ROIs to disk
as a permanent record of your definition of the lesions.
- You are now ready to progress to the next scan to be
measured. Proceed from step 1.