Perfusion and Dynamic Contrast-Enhanced MRI (DCE-MRI)

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.

  • 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 (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

  • 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:

    • Different 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 open and using the file chooser to select the input image, or by pressing the right mouse button and selecting from the menu of recently-used images.

    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.

dynamic_input_setup_multiple_input

The panel below the "Input images:" label shows the current list of selected input images. You use the:

  • select_images_button button to select a new set of images and put them to this list.
  • add_images_button button to select a some more images and add them to this list.
  • remove_all_button button to remove all the images from the list.
  • remove_selected_button button to remove the selected the image(s) from the list (you must first click image(s) in the list to select them).

  • move_up_button and move_down_button 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).

  • 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 standard output image masking options using the Brain Finder, a mask image, or ROI mask.

  • 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. If you select this option, a new set of images will be created on disk with the same name(s) as the input images(s), but prefixed by the letter "r". These images are the registered images, and can later be used to check the quality of the registration (for example, by playing in a movie loop). You can also use them as input images if you want to repeat the perfusion or DCE-MRI without going through the registration process again. Note: this in-line registration procedure only corrects for in-plane rotations and translation. If the subject motion is more complicated, with out-of-plane translation and rotations, you should pre-process the images using the Time-Series Registration tool. Then you will have more control over the degrees-of-freedom for motion correction.

  • 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. If you select this option, please also set the strength of the blur by setting the full-width at half-maximum (FWHM).

  • 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.

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.