1. To prepare the step, we load a Talairach VMR dataset
2. We open the “Segmentation” tab of the 3D volume tools
3. One possible method: use “region growing” and “expansion”
a) We first explore the intensity in the ventricles, which may – depending on the dataset and the previous processing steps, vary considerably.
b) We select a reasonable value range, choose a starting / seeding point in the ventricles and click the “Grow Region” button.
In this case, the result is not to impressive, but not bad either, because we can use the “Expand” function to nicely select neighbouring voxels in the ventricles.
c) We increase the max value in the intensity range
d) Clicking the “Expand” button multiple times will provide us with a larger selection of venticle voxels. Because the result is still not sufficient and apparently restricted to the left hemisphere ventricle, we have to work a little more.
e) We find that the yet nonselected voxels have e.g. an intensity value of 0, so we adapt the minimum intensity range and use again the “Expand” button.
f) We still have to take care of the right hemisphere ventricle. We click into the right ventricle and use the “Grow Region” button.
g) Now it is advised to evaluate the result in three dimensions, e.g. to slice the data from top to bottom. We find that the posterior part of the left ventricle has not been filled.
h) We can use again the “Expand” option to proceed.
i) After several clicks, a satisfying result is reached.
4. To use the manual ventricle filling, we have to switch off the automatic filling of ventricles in the Automatic Segmentation dialog:
5. Running the segmentation will automatically colorcode the previously marked ventricles quite early in the process.
6. Additional remarks:
The ventricle filling can also be performed on the basis of first using the drawing tool and combining this with expansion later.
To avoid erroneous selection of voxels outside the ventricles, the bounding box can be set around the ventricles. To find the proper coordinates, one has to explore the data with the mouse and note the x-, y-, and z-values.
When a brain peeling has been performed before, it is “dangerous” to use the absolute intensity minimum (0) because the demarcation may easily “spill over” to the regions outside the head.
Because there is no “undo” button available, one will always have to reload all. So it is generally better to be a little careful. Ventricle filling should in most cases not take more than a few minutes.