If working with a small portion of a CT scan, it is best to crop the area before you start working with the scan. Crop carefully as you cannot un-do. If you crop something you did not mean to take out, you will ahve to re-load the data.
To create 3D CT models using Amira, first launch Amira. Once it is open, under file, select open data. Navigate to the location of your dicom files and select all of the dicom files associated with the scan of interest. Hit Load.
A dicom loader window pops up with information about the number of files, thickness of the scan slices, etc. Hit OK.
In the top right box of the screen, a green bubble will appear with your scan name in the text (in the example below MULTI SPECS is the name of our scan).
Click on this green bubble and create an isosurface by clicking the isosurface button. After creating an isosurface, right click on your green bubble, choose labeling then label field. You will notice that next to "Pool" a tab appeared that is called "name of your scan - labels"
Click on this new tab. You will be taken to a new window with four panels. The top left panel is your Pool view, the other panels contain the slices of the CT scan.
To create the model you will use the paint tool. This is the paint brush icon under the tool heading.
Select the paint tool and adjust the brush size to desired diameter. Scroll through the slices of your scan and paint over the area of interest for a single material. In the example below, we are making a model of the humerus and a model of the coracoid, which are both in the same scan. The first material will be the humerus, so I will go through and paint over the humerus in the entire scan.
Use the page up or page down key to jump 5 frames. You can jump ahead, paint the frame you jumped to and hit ctrl i to fill in the 5 frames that you skipped. The interpolation is not always perfect, so it is a good idea to scroll through the slices to check the interpolation once your object is painted.
Once the material is painted through the entire scan, you use the stack tool under the selection heading by pressing the icon that looks like a plus sign. Repeat this process for every material of interest. Create a new material by clicking on the New button next to Materials. In the example below, there were many materials created so each piece could be exported independently.
Before you press the stack button, make sure that the material you painted is the material selected in the menu on the right hand side of the window. This is important when creating multiple materials. To re-name a material, double-click on the default name and type in the new name.
Click on the "Pool" tab. Right click the green bubble with your scan name in the text, choose compute then arithmetic. A red bubble will appear, right click on the box in this red bubble and set input B to the green bubble that says -labels at the end of the text. The following options will appear under Properties. In the box next to Expr: type in (B==n)*A, where n=the number of the material in your list of materials for which you want to create a model for. From the example of multiple materials in the iguana scan above, if I wanted to create a model of the sternum, my n would equal 4, since the sternum was the 4th material I created when painting the scan. Hit Apply.
A result bubble will appear. Right click on this bubble, choose display then isosurface. An isosurface bubble will apprear. The following options will appear under Properties. Adjust the color of the surface by clicking on the bar next to colormap. The boxes should both be checked next to downsample and compactify. Hit Apply. The surface will now appear the the view. Adjust the threshold until the model looks accurate. Hit Apply after every adjustment to see the result.
To save as an .obj file, click on the isosurface bubble of the material of interest, hit the "more options" button under Properties, select create surface. A new bubble will appear called Result surf and will not be connected to any result, arithmetic, or isosurface bubble. Click on this new item, go to file and save as. When saving, choose .obj as file type.