How to Adjust the 16-Bit CLUT (Color Look Up Table) Editor in OsiriX 1. Import the series you are interested in into the 2D/3D Viewer. I m using the OBELIX data set, slices 1-395, available for download from the DICOM Sample Image Sets. This is a CT data set with contrast. 1a. It should be noted here that if you are using a data set that you have modified previously, the modifications may still be applied to your data. This may or may not cause a problem when editing in the 16-bit CLUT. To ensure a clean slate, you may want to go to File -> Rebuild Selected Thumbnails, after clicking on the series you need.
1b. Or select File -> Rebuild Database to refresh all of the cases. 2. Under the 2D/3D pulldown, open the series into the 3D Volume Render. 3. There are three pull down menus that you may or may not have noticed before. The one that we are currently interested in is the CLUT - color look up table. While there are numerous presets that can be cycled through at your leisure, we are going to concentrate on the 16-bit CLUT Editor. All of the other presets are in an 8-bit style, and the 16-bit color selection allows for a little more control over the transparency and color selections within your data set. So, go ahead and select that option.
4. Okay, this is usually what initially pulls up after the program thinks for a little while. First off, we can see that there is a graph along the bottom of the screen that has never shown up before. Also, there is a colored curve automatically drawn, with a few points along it s curve. We ll be getting to these in more detail later. 4a. The graph can be divided along it s x and y axis, with different elements becoming more prominent as you move along in any direction. x-axis: this maps out the image in a linear fashion along a density scale. In other words, to the far left the graph represents air. And to the far right, it represents very dense matter, such as bone or areas of very high contrast. So, generally from right to left (which is generally how I think of graphs, as more of what I am interested in seeing is on the right) we have: bone, contrast material, vessels, highly vascularized tissue (i.e. organs such as the kidneys), soft tissue, skin, air. y-axis: this is the transparency function. The top is completely opaque, running down to completely transparent at the bottom. The values for this are 0 (bottom) to 1 (top). Setting a curve at the arbitrary position of 1 can cause unsightly artifacts to appear as the data can become too opaque, so some manipulation is required to find the best setting.
4b. The curve that lies on this graph defines the area of your data set that is visible. This curve can be manipulated in two major ways. 1: the black square in the middle of the curve allows you to move it either left/right or up/down along the x or y axis of the graph. This is a quick way to change the overall area defined or the transparency. For example, if you want the skin defined, you move the entire curve more the left. However, if you are looking for bone and vessels, move the cure more to the right. Likewise, move the curve down if you want that tissue to be more transparent, and up for more opaque. 2: the individual points along the graph can also be changed to further refine the area of the data set that is visible. Like the black square, they can be individually moved so that certain colors define certain tissue densities, and how transparent those colors will show up as. By clicking on the point once, a small dialogue box shows up. This directly lists the x and y position - the position along the x-axis for that specific point and alpha (transparency) setting. Clicking the black square in the middle will bring up this dialogue box for multiple points along the curve. While the data within this dialogue box cannot be edited, it does allow for a more precise editing of points. 5. These points can be further modified, allowing you to change the color of the curve. Double click on a point to bring up a color wheel editor. As you manipulate the color in the color editor, the data set reflects these changes in real time.
Now, I m going to go ahead and make some modifications to the data set we have selected. 6. Right away you can see that the data has changed. At the beginning of step 4 with the default curve, we had some bone, soft tissue, organ, and vessel information showing up. Here, I ve manipulated the curve and changed the color in order to highlight just the bones, as close to just the bones as possible. (Due to the contrast agent, the ureters, part of the renal pelvis, and the bladder are also still visible.) Let me explain specifically what I did. By double clicking on the individual points, I made color changes. I wanted the bone to have more of a cooler color, not quite white/gray. So, I made the point to the far right a greenishwhite, moving to a white at the second point. Then, there is a quick falloff to a reddish-pink color that is along the part of the graph closest to where the soft tissue will begin to show up. This allows for a more natural color gradation. Secondly, I ve manipulated the curve position. I ve brought the first point out to the far right (about x position 1243). This allows everything under the area defined by the curve to show up. Because everything to the right is bone, I wanted all of it to be selected and visible. I also moved the points higher on the y-axis to give the bone a more solid feel (remember higher on the y-axis is more opaque, so the alpha is set around.625). This is where the fact that a setting of 1, or the top of the graph may be too much opacity. The two points to the left begin the fall off. It can be tricky to define the specific area of bone vs. soft tissue, so by moving that point to a slightly more transparent area, it allows the bone to retain most of it s integrity without bringing out too many hot-spots of unwanted tissue. The final point to the left defines the shadows of the data set. This point is default black, and I generally leave it along the bottom to give better definition to the shadow areas. However, feel free to play around with any of these settings to see what they produce. 6a. As you can see, this is the same curve - but I ve moved it down on the y-axis (alpha setting of.24). The positions of the points along the x-axis have not changed. By moving it down on the y-axis, the data set defined by this curve becomes more transparent.
7. Now, here is something that makes the 16-bit CLUT very powerful. This algorithm has the ability to define multiple tissue density curves. Right click on the graph area and click on New Curve. 8. As you can see, this pulls up another default curve that can then be edited to define a tissue that you wish to highlight. In this case, why don t we go ahead and pull the bone transparency back up so that it is opaque. And lets change that new curve so that it better defines just the internal anatomy, specifically the vessels and kidneys.
9. Okay, here is that data set, now with the two curves mentioned. I also changed the colors on the bone curve to better differentiate the cool bone from the warmer vessels. I moved the new curve behind the bone curve to try and bring out the cooler colors of the bone better. This option is available when you right click, select Send to Back. Note: The send to back option sometimes causes data to rearrange itself, but more often, it is a very subtle change. At times, it causes no visible effect at all. 10. Now, to further demonstrate the versitility of this 16-bit CLUT option, we are going to add another aspect of the anatomy. Right now, we are looking at how the bones interact with the vessels and internal organs. Lets go ahead and add the surface anatomy as well. This can give a good reference for illustrations. Right click on the graph area and select New Curve once again.
11. As you can see, I ve already manipulated the curve as we talked about in the previous steps. This is a fairly narrow band, as the tissue density of skin doesn t encompass much. If you want to get technical, you can see that it actually coincides with the last peak to the left before the sharp drop-off (around x value -100). As you use this graph more, the areas that define different tissue densities become more clear. At this level of opacity, you can better see where the areas of skin are going to be defined. However, we can no longer see the internal anatomy. This is more of a confirmation that you have the correct area selected. 12. Here we can see that with the skin opacity brought very low, the bones and internal organs sitting within the abdomen. 13. Once you have settings to a point that you like, you have the option of saving out these settings. Again, right click in the graph area. This brings up that dialogue box mentioned earlier, and click on the Save option. Type in the name you want (I called this one test ) and save.
13a. This allows you to reselect this specific CLUT later, if you want to edit it again. It continues to be an option, even after OsiriX is closed and reopened. However, note that it applies the CLUT without the graph at the bottom. To re-access the graph settings if further editing is necessary, first apply the CLUT from the preset menu. Once applied, reopen the 16-bit CLUT, and the graphs are there for editing at a later date. This option also allows you to save out a CLUT and apply it to multiple data sets. These steps can also define different areas of transparency, such as the lungs transparent over the heart, viewing the skull inside the soft tissue of the face, etc. Many possibilities are open once this tool enters your workflow. I hoped this helped to begin to explain how to utilize the 16-bit CLUT in your OsiriX pipeline. Feel free to e-mail questions and suggestions, corrections, etc. to sarah.hegmann@yahoo.com.