The Angiography tools are closely related to the Diffusion tools as even a cursory look at
the User Interfaces will make easily obvious. The key insight is that given
an angiography image, once the Hessian matrix is computed (at multiple
scales -- this is performed using the Vessel Utility
tool, tracking vessels is fairly similar to fiber tracking. This is
accomplished using the Vessel Tracking Tool.
In general the procedure for extracting vessels is as follows:
- Compute the Hessian Matrix at different scales using the Vessel Utility Tool.
- Use the Hessian as an input to the Vessel Tracking tool to extract vessels.
The Vessel Utility Tool
The Vessel Utility Tool consists of three tabs, the "Input Tab", the "Vesselness Tab" and the "Results Tab", shown above. The general procedure for using this is as follows.- The user specifies the input image and an optional mask image in the input tab. The mask, if used, should be a binary image that encloses the region in which the vessel of interest lie. It is a computational speedup tool.
- Next in the vesselness tab one needs to specify the maximum intensity inside the vessel (top left), and the size of the target vessels (in voxels), which is controlled by the range of scales set in the multi-scale analysis.
- Once the setup is done, pressing the Compute button at the bottom of the image, will generate the output hessian as well as other result files detailed below.
The Input Tab
This essentially is used to specify the input image and the region of interest (mask) image.The Input Image frame is used to specify the raw input image. The "Load" button loads an image from a file. The "Grab" button grabs the currently displayed image in the viewer, whereas the "Display" button sends the input image to the viewer.
The Region of Interest frame is used to optionally specify a mask for the computation of the hessian and associated parameters. There are three options:
- Use the entire image for computation. This is the default and is
accomplished by checking on the "Use Entire Image for Computation" checkbox
and leaving the "Threshold Image at" button to off.
- Use a thresholded version of the image. This is accomplished by checking on the "Use Entire Image for Computation" checkbox
and leaving the "Threshold Image at" button to on and setting an
appropriate threshold.
- Using an external mask. This can be generated using the Segmentation tools. A good way to obtain a mask is to threshold the image at some reasonable level and then dilate the mask somewhat to ensure that no vessels are lost due to locally dark regions. Then ensure that "Display Mask" in the Math_Morphology tab (of the Segmentation Tool) is selected, display the mask and use the Grab button to grab it from the viewer into the vessel utility control.
The Vesselness Tab
The vesselness tab is used to set the detailed parameters for the computation of the hessian and the vesselness measure that is used to select the scale at which the hessian is computed at each voxel (See Jackowski et al for details.)The ``sensitivity'' parameters are used to evaluate the vesselness measure defined in equation (1) of Jackowski et al. The only parameter that needs to be modified is the Maximum Intensity parameter, which should be set to the approximate maximum intensity inside the vessels of interest. The other parameters should not be changed, unless one has specific reasons for changing them.
The ``multiscale'' analysis parameters should be set so as to reflect the range of vessel sizes one is interest in (in voxels). The hessian matrix is computed at a number of scales (e.g. 5 in the example shown) ranging from the minimum vessel size (e.g. 3.0 voxels in this size) to the maximum vessel size (e.g. 8.0 in the figure shown). If the "logarithmic" check button then the scales are concentrated more towards the lower end of the range, otherwise they are evenly distributed.
The ``other processing'' parameters tab has two parameters. If the "isotropic" checkbutton is enabled, the input image is resliced to isotropic resolution (average of all three voxel dimensions) prior to any subsequent processing, otherwise the original image is used. The "Results Smoothing" option menu can be used to enable smoothing of the "Vesselness Measure" and "Maximum Scale Results" to make them more visually pleasing. This smoothing does not affect the computation of the Hessian in any way.
The Results Tab
The results of the processing are stored in the results tab. The key ones are:- The Hessian matrix, which is the key input to the vessel tracking
tool.
- The Vesselness measure, which represents the likelihood of having a
voxel centerline at any given voxel.
- The Maximum scale measure, which represents the most likely estimate of vessel radius (in voxels) at each location. This measure can be error prone and should be used with care.
The Vessel Tracking Tool
The Vessel Tracking tool takes the Hessian Matrix computed from the Vessel Utility tool above as an input and uses fast marching techniques (see Jackowski et al for details.) to extract vessel centerlines. This tool is closely related to the Fiber Tracking tool and the documentation for the Fiber Tracking tool should also be consulted for the vessel tracking tool. In this document, we mostly highlight issues specific to vessel tracking.
Loading the Images
First, you will need to load the hessian image, computed by the Vessel Utility (above). Secondly, load either the anatomical mask you have created earlier or the ROI you would like to use for tracking in the Region of interest mask. Finally load the auxiliary image, which could be either the vesselness or the maximum scale image computed by the Vessel Utility tool, in the Map for analysis box. Once all these input images are loaded, make sure that you have an image in the viewer (e.g. mask, or map for analysis) before you start tracking.Propagation
Once the data is loaded, the next step is to compute the fast marching solution. Switch the control to the "Propagation" tab, and place the viewer crosshairs and the "center" of the region of interest, e.g. in a large vessel. Then press the Compute button. Once the propagation is computed then vessel tracking can be performed.
Tracking
Seed point selection: You may choose to seed the tracking using a single point, a region of interest, a volume, or points from the landmark control. In case of a single point, the position of the cross-hairs in the main viewer will be used as coordinates for the point. In case of a region of interest, you must specify the region number to start tracking from. All points from the ROI will be used as seeds. You can also increase the point density. For volume, a 3D window of size Width x Height x Depth is taken to initialize the tracking.Integration Parameters: The integration method used by the Fiber Tracking program is
the well known Runge-Kutta. You may specify second-order or forth order
integration, which provides better accuracy. The step length (h) for integration represents the
percentage of a voxel diagonal's length. Higher percentages will yield
coarser results while smaller values will yield smoother vessels.
Once you made sure the relevant parameters were set, simply press the Track! button to start tracing.
Vessels
Once tracking is complete, you are taken to the Vessels tab, in which the tracing results will accumulate. Vessel names and colors can be changed, simply select a vessl from the list and either change the label or press the color button. They can also be made visible or hidden by clicking the Display checkbox. You can save a vessel or a set of vessels by selecting them from the list and pressing the Save button. Note that you will be prompted for a directory name for saving. The vessels are saved according to their label names. To save a vessel with a different name, you must change its label first.Important!
The Vessels are not immediately visible in the viewer, until you switch the viewer to 3D mode, and select View Vessels under the Display tab. For more information on the "Display" tab see the documentation for the Fiber Tracking tool.