AMIDE tutorial

AMIDE home page

Credit for AMIDE belongs to Andy Loening who has made this opensource development.  AMIDE can open a large number of different file formats, although some of the bugs are still being ironed out of them.  This tutorial shows how to view CT data with AMIDE as a virtual radiograph which can be looked at from any angle.  Digital removal of items such as plaster is also done.

Screenshots at various points along the track are included and menu commands are in courier font.

Opening the file


The initial AMIDE window



I find that Importing a ".raw" file to be the easiest way to work in AMIDE.  I use VolView to convert a DICOM stack into a .raw file - this also puts out a small text file with a .raw.vvi tag which can be opened by any text editor.  The data on voxel numbers and sizes is all contained in the .raw.vvi file.  One uses the parameters in the .raw.vvi file in the "import file" dialog to import all the data - the data type from our Phillips CT scanner is "Signed Short, Little Endian (16 bit)  - you may have a different data type depending on your data source.  The numbering in the .vvi file starts at zero, so when typing in the number of voxels into the open file dialog, remember to add one.

File>Import File(specify)>Raw Data













Once in the main AMIDE window, the first thing that I often do is crop the volume so that less memory is needed for subsequent operations.  A crop wizard allows you to see what you are trimming off in three planes.

Tools>Crop Active Data Set









Removal of extras


AMIDE has a 3D range of interest (ROI) algorithm attached that is useful for cutting off plasters and CT scanner tables.  The ROI algorithm works best for high contrast subjects and so setting of the color maps to high contrast makes for easy work.

Set thresholds icon on toolbar - rainbow colored



Right click in the study window and choose "Add a new 3D isocontour ROI" from the pop-up menu.

[right click]
>Add a new 3D Isocontour ROI
or Edit>Add ROI>3D Isocontour



Clicking on the edge of the structure you want to remove then generates a nice 3D ROI that hopefully includes all of the area that you want to excise.   The algorithm is quite finicky as to exactly where you click and you may need to try a few times before you get exactly what you want.



If the 3D ROI is correct, all you need to do now put the pointer over the ROI line and right click whilst holding the ctrl button down - this sets the value of everything in the ROI to zero.

[ctrl]-[right click] on ROI line








Normalizing the contrast should be done before proceeding to volume rendering.

Set thresholds icon on toolbar - rainbow colored




It is a good idea to save your work at this stage as an .xif file that AMIDE uses.

File>Save As...


Viewing

The next step is to request the volume rendering window.  If the volume rending window fails to be created, I have found that using a smaller volume (by using the shrink  filter in VolView) or re-cropping the volume allows the computer to work properly.



Setting the rendering parameters allows for alteration of rendering quality and stereo seperation.  Using a slower computer/graphics card combination, changing the "Speed versus Quality" button to suit will save you a lot of time.  The Highest Quality and Slowest option renders all voxels in the volume, where the High Quality and Medium Speed option skips voxels with a density under 1% - making it considerably faster.

Edit>Rendering Parameters>Speed versus Quality








The opacity and density transfer functions are set using the left-most icon on the toolbar.

Setting the "Return Type" to opacity sets us up to render based on opacity.  "color table" can be set to whatever you fancy but to show a traditional radiograph, set this to "black/white linear".



The "Gradient Dependent Opacity" can be set to a flat line.



The first point along the x-axis on the "Density Dependent Opacity" detemines the cut off between what is visible and what is not.  I usually set this to the point where soft tissue just dissappears.



The rest of the "Density Dependent Opacity" can be modified to suit.  It is easiest and the least computationally expensive to set it to somewhere along the far right axis, though you can play around with it as much as you want.




Stereo viewing is done by clicking on the double eye on the toolbar.  This generates a parallel view stereo rendering which you can move around in synchrony.



Again, thanks to Andy Loening.

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Ezekiel Tan
Mar 2004
v.1.0