Dynamic Analysis - Introduction

In this context, dynamic scanning refers to the use of contrast agents in MRI or CT scans, where the passage of the contrast agent is monitored by repeatedly acquiring the scans. These can be either T₁-weighted or T₂*-weighted MRI scans, or x-ray CT scans.

T₁-weighted images are typically used in dynamic contrast-enhanced MRI (DCE-MRI) to monitor the concentration of contrast agent as it leaks from the vasculature into the extra-cellular interstitial space of the tissue.
T₂*-weighted MR images, or dynamic CT scans are typically used in brain perfusion studies to monitor the concentration of contrast agent in the vasculature as it passes through the brain tissue.

The two tools used to analyse these different sorts of scan have a great many similarities, and are described together in this Chapter. For both tools, the concentration of contrast agent is assumed to be proportional to the change in relaxation rate in the tissue. Analysis is normally performed pixel-by-pixel, but the DCE-MRI tool can also analyse dynamic parameters within a region of interest.

Start the Brain Perfusion tool or DCE-MRI tool from the Toolkits menu.

Some of the setup is common to both tools. The setup for organising and pre-processing the input images, and setting up the output images is common, and these are described below below.

Input Images

Threshold. This is a way to prevent processing of pixels in the background noise. To do this, enter an intensity value. If the pixel intensities at each location for all time points are below the threshold you set, then the intensity in the resulting output images at that location is set to zero.
The images that are to be analysed consist of a time-series of images, which may be from a single slice location or multiple slice locations. These may be organised in one of three ways, and you must tell the analysis tool in which way they are organised.
- Multiple input images (one per time point). You have as many input images are there are time points. Each image contains all slice locations that you want to analyse.
- Multiple input images (one per slice location). You have as many input images are there are slice locations. Each image contains all time points.
- Single input image (all time points and all slices). You have just one input image. This image contains all the data (all slices and time points) to be analysed. If this is the case, then you must also tell the tool about the ordering of data within this image:
  - Time points are contiguous in image file. Select this option if the ordering of slices has all time points for the first slice location followed by all time points for the second slice location, etc.
  - Different slice locations are contiguous in image file. Select this option if the ordering of slices has all slice locations for the first time point followed by all slice locations for the second first time point, etc.
  Select the single input image by clicking on the and using the file chooser to select the input image.
  You must also tell the tool how many time points are in the image so that it can distinguish time points from slice locations.
If you selected either of the first two options (multiple input images), then the window changes appearance to that below.
The panel below the "Input images:" label shows the current list of selected input images. You use the:
- button to select a new set of images and put them to this list.
- button to select a some more images and add them to this list.
- button to remove all the images from the list.
- button to remove the selected the image(s) from the list (you must first click image(s) in the list to select them).
- and buttons to move the selected image(s) up or down the list. Images must be in the correct order for analysis - either in the correct slice order, or in the correct time order. Use these buttons to reorder them if they are not.
The time between subsequent images in the acquisition (in seconds).
The number of steady-state images. Some pulse sequences need a few scans to be acquired in a dynamic series before a steady state of magnetisation is reached. If this is the case, the tool can discard the first few time points by entering an integer number of time points to discard.
Whether you want to perform an image registration as a pre-processing step. If you select this option a rigid-body registration will attempt to correct for patient motion between the different time points. This is quite time-consuming, so you may want to perform the analysis without registration first to check that your setup is correct.
Whether you want to spatially filter the images as a pre-processing step. If you select this option, a 2-D Gaussian blur will be applied to your input images before calculation of dynamic parameters. This effectively reduces the spatial resolution, but can improve results where signal-to-noise ratio is poor.

Image Output

Both the brain perfusion and DCE-MRI analysis tools produce several parametric output images. The name of the output parameter is appended to a "base" image name. You choose the base output image name by clicking on the

icon, or typing in the directory and file name. N.B. These tools will not overwrite existing output images.

Saving Settings

If you want to perform several similar analyses, you can set up the tool to your requirements, then press the

button. Then, next time you start the tool, it will be configured in the same way. To revert to the default settings, press the

button.

Having set up your input and output images, you can go on to perform either the brain perfusion or DCE-MRI analysis.

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