Perfusion and DCE-MRI Analysis - Introduction

For perfusion and dynamic contrast-enhanced MRI (DCE-MRI), contrast agents are used 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.

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 (for MRI) or the change in density (for CT). 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.

toolkits_brain_perfusion toolkits_dce_mri

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.
Input Images

perfusion_input_setup

Image Output

dynamic_output_setup

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 open icon, or by typing in the directory and file name.
Note: these tools may overwrite existing output images, depending on the type of output image, and the setting of the overwrite preference.
Saving Settings
If you want to perform several similar analyses, you can set up the tool to your requirements, then press the save_settings_button button. Then, next time you start the tool, it will be configured in the same way. To revert to the default settings, press the set_defaults_button button.

Alternatively, if you have several different analysis setups that you want to work with, you can save the whole setup as a "preset". Select "Save as Preset ..." from the "Presets" menu. Then, when prompted, enter a title for the preset - this will be the name given to the preset when it is put into the Presets menu. At any future time, you can then recall the whole setup by selecting the preset title from the Presets menu.

You can delete presets by selecting "Manage Presets ..." from the "Presets" menu.

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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