Cross-Sectional Analysis

The picture below shows the setup for assessing brain atrophy at a single time-point (cross-sectionally) using just a T1-weighted image.

Setup for cross-sectional brain atrophy assessment

The input image should, ideally, have been acquired using a 3-D (not multi-slice) pulse sequence. Follow these steps for cross-sectional atrophy assessment:

  1. Load the T1-weighted image in the input image selection panel. In the example above, this is called "T1Weighted.nii".
  2. Optional. If you want to use a FLAIR image as well, increase the number of contrasts to 2, and select the FLAIR image.
  3. Leave the The Markov Random Field regularisation strength slider slider at its default value of 5. This should not need to be changed.
  4. 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).

  5. For:

    Skip,

    Selecting regularisation

    see the processing options section.

Now press the Button to start the atrophy analysis button to start the analysis, which will take a few minutes. When the analysis is complete, you will see a pop-up message showing the results:

Results for cross-sectional brain atrophy assessment

These results show:

  • 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 grey-matter fraction (GMF), which is: GM Volume / ICV.
  • The white-matter fraction (WMF), which is: WM Volume / ICV.

To make a permanent record of these results, 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.
  • 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.

For an input image called "T1Weighted.nii" and a base name of "Test", these output images will be created in the selected folder:

  • TestGMPrior.nii - the grey-matter prior probability image, registered to the T1-weighted image.
  • TestWMPrior.nii - the white-matter prior probability image, registered to the T1-weighted image.
  • TestCSFPrior.nii - the CSF prior probability image, registered to the T1-weighted image.
  • TestLVPrior.nii - the lateral ventricles prior probability image, registered to the T1-weighted image.
  • Test.rtp - the registration transform parameters that transform the template image to the T1-weighted image.
  • rT1Weighted_pGM.nii - the grey-matter posterior probability image.
  • rT1Weighted_pWM.nii - the white-matter posterior probability image.
  • rT1Weighted_pCSF.nii - the CSF posterior probability image.
  • rT1Weighted_pOTHER.nii - the other (non-tissue) class posterior probability image.
  • rT1Weighted_Classes.nii - a colour image showing the final segmented tissue classes.
  • rT1Weighted.nii - a cropped version of the T1-weighted input image and bcrT1Weighted.nii, a bias-corrected version of this.

The procedure for cross-sectional atrophy assessment is summarised in the flow-chart below.

The flow chart for cross-sectional brain atrophy assessment

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.