Dynamic Analysis

Introduction

Often, a series of images is acquired where the signal intensity change through the series of images must be analysed. Examples of these types of acquisition include functional magnetic resonance imaging (fMRI) and arterial spin labelling (ASL), but there are many other possibilities. The Dynamic Analysis tool in Jim is a general tool for the analysis of a series of images where the signal changes through the series.

The Dynamic Analysis tool contains two modules for analysis, but is easily extendable using your own plugins that you can write using the Java programming language.

Start the Dynamic Analysis tool from the Process menu.

This brings up:

Some of the setup is common to all forms of analysis. 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

• The images that are to be analysed would normally 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 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.

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 standard input image masking options using an intensity threshold, 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. When selected, 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 analysis 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

All forms of analysis produce one or more parametric output images. The name of the output parameter(s) is appended to a "base" image name. You choose the base output image name by clicking on the 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 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 dynamic analysis.