Quasi-Automatic Cord Follow-Up

The quasi-automatic Cord Follow-Up tool can estimate the change in spinal cord atrophy between two time-points almost automatically from a pair of T₂-weighted images. It works similar to the semi-automatic mode, but there is much less user-interaction.

Start the Cord Follow-Up tool from the Toolkits menu: Then for quasi-automatic cord follow-up, ensure that the checkbox is selected.

The Cord Follow-Up tool will now appear as shown below:

Note that the ROI Toolkit also pops up when you start the Cord Follow-Up.

Processing is similar to Cord Follow-Up tool in semi-automatic mode. The differences are:

• For each of the two time-points, the images may be in any orientation (axial/coronal/sagittal), although of course they should have been acquired in an identical way (same pulse sequence and slice positioning).

• Create two ROI files, each containing a single Marker indicating the position of the C2/C3 disk, as for the quasi-automatic Cord Finder.

Save the Marker ROIs into ROI files that have have a base names which are the same as the image to be analysed. For example, if you are analysing a images called BaselineCord.nii.gz and FollowUpCord.nii.gz, the ROI files must be called BaselineCord.roi and FollowUpCord.roi.

• Select the most superior landmark in the "First landmark" panel, and the most inferior landmark in the "Final landmark" panel. The cord cross-sectional areas and volume will be assessed over the length of cord between the first and final landmarks. You can select any pair of landmarks between the odontoid process of the epistropheus (OPE) and the T4/T5 disk. However, if these anatomical landmarks are not present in the both the images because they are outside the field-of-view, then you will see an error message part way through processing.

If you select the same landmark in both the "First landmark" and "Final landmark" panels, then the panel below is shown for you to set the thickness of a slab of slices centred on that landmark.

You can set the slab thickness between 1 and 41 mm, in steps of 2 mm, which is positioned so that the cord assessment landmark is always in the central slice of the slab.

Then set:

• This determines the smoothness of the cord outline: using a small number will give cord shapes that are smoother, while using a large number will give shapes that are more capable of following a more complicated outline shape. We recommend you use 24 coefficients, and only reduce it if the outlining becomes erratic when the images have poor contrast-to-noise ratio, and only increase it if the outlines found are excessively smooth and do not follow the shape accurately in all slices.

• The Cord Follow-Up tool co-registers the straightened images of the cord at the two time-points. By default, it performs a fine spline-based deformation to obtain the best alignment. If you find this to be unreliable, you can disable this fine registration by selecting this check-box.

• By default, the Cord Follow-Up tool outputs straightened cord images in the half-way registered space only for the forward registration direction. When this check-box is selected, images for both forward and reverse registration directions are output, together with the corresponding cord outline ROI files.

  The half-way straightened cord images and corresponding cord outline ROI files will be prefixed by hwFwd for the forward direction, and hwRev for the reverse direction.

Press the button to start the analysis.

The cord cross-sectional areas will now be assessed, along with the change in area as a measure of progressive cord atrophy. Depending on the extent of the spinal cord segment being evaluated and the speed of your computer, processing will take around 20 minutes. When complete, you will see the results in a dialog like the one below:

This shows:

• The mean spinal cord cross-sectional area assessed at the first time-point.
• The mean spinal cord cross-sectional area assessed at the second time-point.
• The percentage change in spinal cord volume from the first time-point to the second assessed in the forward direction.
• The percentage change in spinal cord volume from the first time-point to the second assessed in the reverse direction. This is calculated by interchanging the first and second time-points, rerunning the analysis, and negating the percentage change.
• The percentage change in spinal cord volume as the average of the forward and reverse directions.

To make a permanent record of these results, showing more detail, 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.

As well as the results above, a report will detail the the cross-sectional areas at regular intervals (in steps equal to the original slice thickness) down the cord, for both time-points, and produce a graph showing the same. The cross-sectional areas are measured in a plane that is perpendicular to the local cord centre-line.

The following images and ROI files are produced:

• An axial straightened cord image (with the suffix _Cord appended to the input image name) for each of the 2 time-points. These images include the cord region covering all the identifiable Landmarks (OPE to T4/T5) that are present in the input images.
• Two ROI files containing the landmark Markers for each of the anatomical landmarks (OPE to T4/T5) that are found on the input images. These ROI files can be loaded onto the respective straightened cord images, to verify and correct Landmark positioning.
• Two straightened cord images at the half-way registered location. These have the same names as the input images but with the name prefixed by "hw" (half-way). The images cover the cord between the Landmarks selected by you as the cord assessment region.
• Two ROI files containing the cord outlines, with file names matching the half-way registered images.

Below are images of the cord acquired 1 year apart, with the cord registered to the half-way location, and with the cord outline ROIs loaded.

Baseline cervical cord and segmentation	1 year follow-up cervical cord and segmentation