Longitudinal Analysis

The picture below shows the setup for assessing changes in brain atrophy over time, using T1-weighted images.

Setup for longitudinal brain atrophy assessment

The input images must have been acquired using the same MRI scanner and imaging protocol at every time-point. Follow these steps for longitudinal atrophy assessment:

  1. Set the number of time-points using the Spinner to set the number of time points to be analysed spinner. In this example, there are two time-points, but you can set this to more than two if you have more follow-up images.
  2. Load the T1-weighted images in the input image selection panels. In the example above, these are called "BaselineT1.nii" and "FollowUpT1.nii" for the two time-points. These images should, ideally, have been acquired using a 3-D (not multi-slice) pulse sequence.
  3. Optional. If you want to use FLAIR images as well, increase the number of contrasts to 2, and select the FLAIR images.
  4. Leave the The Markov Random Field regularisation strength slider slider at its default value of 5. This should not need to be changed.
  5. Set the base name and folder for the output images. The base name is used to construct the name of some of the output images (see below).

  6. For:

    Selecting whether to skip skull-stripping and registration pre-processing steps,

    Selecting whether to provide extra regularisation when diffeomorphically registering the template image to the T1-weighted imput images see the processing options section.

Now press the Button to start the atrophy analysis button to start the analysis, which will take some time. When the analysis is complete, you will see a pop-up message asking which type of report you want to create:

Save the results of the longitudinal brain atrophy assessment

You can:

  • Write to a text file report. A File chooser will appear, for you to choose a log file name. The default file extension for log files is ".log". If the chosen file already exists, an entry will be appended to the log file.
  • Write to a PDF file report. A File chooser will appear, for you to choose a PDF file name. If the chosen file already exists, an entry will be appended to the PDF file. A PDF report will also include an illustration the GM/WM/CSF segmentation at each time-point.
  • Send a PDF report to a DICOM server. The DICOM server to which it will be sent must already have been set up, and is the current server selected in the DICOM Query/Retrieve tool. See these instructions for how to set up the connection to remote DICOM servers.
  • Save PDF and Send to DICOM. Both save to disk and send to a DICOM server.

The report will show, for each time-point:

  • The white-matter (WM) volume.
  • The grey-matter (GM) volume.
  • The cerebro-spinal fluid (CSF) volume.
  • The intra-cranial volume (ICV), which is the sum of the volumes of the 3 compartments above.
  • The brain parenchymal fraction (BPF), which is: (GM Volume + WM Volume) / ICV.
  • The white-matter fraction (WMF), which is: WM Volume / ICV.
  • The grey-matter fraction (GMF), which is: GM Volume / ICV.

Also shown for each pair of time-points:

For input images called "BaselineT1.nii" and "FollowUpT1.nii", and a base name of "Longitudinal", these output images will be created in the selected folder:

  • LongitudinalWMPrior.nii - the white-matter prior probability image, registered to the average co-registered T1-weighted images.
  • LongitudinalGMPrior.nii - the grey-matter prior probability image, registered to the average co-registered T1-weighted images.
  • LongitudinalCSFPrior.nii - the CSF prior probability image, registered to the average co-registered T1-weighted images.
  • LongitudinalLVPrior.nii - the lateral ventricles prior probability image, registered to the average co-registered the T1-weighted images.
  • Longitudinal_Det1_2.nii - showing the determinants of the Jacobian for the deformation that maps the first time-point to the second.
  • rBaselineT1.nii and rFollowUpT1.nii- co-registered versions of the input images produced during Part 1 of the processing (see below).
  • bcrBaselineT1.nii and bcrFollowUpT1.nii- co-registered and bias corrected versions of the input images. Bias field correction occurs as a side-effect of the Expectation-Maximization algorithm.
  • rBaselineT1_pWM.nii and rFollowUpT1_pWM.nii - the white-matter posterior probability images for the two time-points.
  • rBaselineT1_pGM.nii and rFollowUpT1_pGM.nii - the grey-matter posterior probability images for the two time-points.
  • rBaselineT1_pCSF.nii and rFollowUpT1_pCSF.nii - the CSF posterior probability images for the two time-points.
  • rBaselineT1_pOTHER.nii and rFollowUpT1_pOTHER.nii - the other (non-tissue class) posterior probability images for the two time-points.
  • rBaselineT1_Classes.nii and rFollowT1_Classes.nii - colour images showing the final segmented tissue classes at each time-point.

The procedure for longitudinal atrophy assessment is summarised in the two flow-charts below.

The flow chart for part 1 of the longitudinal brain atrophy assessment
Part 1 of Longitudinal Atrophy Processing

Part 1 involves co-registration of the T1-weighted images images and averaging to provide a registration target for the (optional) FLAIR images.

The flow chart for part 2 of the longitudinal brain atrophy assessment
Part 2 of Longitudinal Atrophy Processing

In Part 2, the template tissue class prior probabilities are registered to the average T1 and these, together with the co-registered T1-weighted and optional FLAIR images are input to the Expectation-Maximization classification algorithm.

The red arrows indicate a registration step, with the arrow pointing towards the registration target. The use of the FLAIR image is optional. E-M: expectation-maximization classification algorithm.