Cord Follow-Up
The Cord Follow-Up tool is used for estimating the change in spinal cord
atrophy between two time-points.
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.
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.
- 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.
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 forward 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.
You can create a more detailed report by clicking on the
button (to a get a report in text format) or
the button to get a report in
PDF format. Click the
button if you do not want a detailed report.
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, with the cord outline ROIs loaded.
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Baseline cervical cord and segmentation |
1 year follow-up cervical cord and segmentation |