Semi-Automatic Cord Follow-Up

The Cord Follow-Up tool can estimate the change in spinal cord atrophy between two time-points. The Cord Follow-Up tool first straightens the cord, then co-registers straightened cord images from the two time-points in a half-way registration space, and performs cord outlining for each of the two time-points in this registered space. The tool performs the analysis twice: once by registering the second time-point to the first, and then again by registering the first time-point to the second. This is done to reduce bias in the registration process. As an aid to visualising the results, the half-way registered straightened cord images are written to disk, together with the corresponding cord outline ROI files.

By default, the registered straightened cord images are only output for the forward registration direction (second time-point registered to the first), although there is an option to output registered images for both directions.

Start the Cord Follow-Up tool from the Toolkits menu:

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.

For semi-automatic cord follow-up, ensure that the checkbox is not selected.

You can assess the change in spinal cord atrophy between two time-points in a similar way that you assess cord cross-sectional areas for individual scans. Prepare the images at each time-point as you would for the Cord Finder tool.

• For each of the two time-points, load the axial cord MRI scan into Jim's display and place Marker ROIs at regular intervals down the cord centre-line, as you would for the Cord Finder tool.

• Save the ROI file with their default file names (the same as the image name but with the file extension .roi).

• Set the nominal cord diameter, number of shape coefficients and order of longitudinal variation as you would for the Cord Finder tool.

• Select this if you are working with T₂-weighted images. If working with T₁-weighted images, then leave this unchecked. It is NOT recommended to use T₂-weighted image, since the reliability of the Cord Follow-Up tool has not been tested with T₂-weighted images.

• 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.

• You can save the deformations that have been found that align the two cord images, and apply them to other pairs of images. However, for this to be successful, the second pair of images must have exactly the same geometry as the corresponding first pair of images (i.e. the image at time-point 1 used to find and save the deformation must have the same geometry as the image at time-point 1 to which the deformation will be applied; and the same for the pair of images at time-point 2).

  

• To save the deformations, select the "Write transforms to file" check-box, and enter the name of an XML file to which the transforms will be saved.

• To apply the deformations to another pair of images, select the "Apply transforms" check-box, and enter the name of the XML file that was previously saved.

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.

Also produced are two straightened images of the cord, registered to their half-way location; these will have the same names as the input images but with the name prefixed by "hw" (half-way). The cord outlines are saved to ROI files with names taken from the input image name but prefixed by "hw", and suffixed by "_cord.roi".

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