Cord Finder - Introduction
The Cord Finder tool can be used to isolate the spinal cord on MRI spinal cord scans, and to
calculate the cross-sectional areas along the cord, perpendicular to the cord axis.
Start the Cord Finder tool from the Toolkits menu: 
The Cord Finder tool will now appear as shown below:
Note that the ROI Toolkit also pops
up when you start the Cord Finder.
The procedure for outlining the cord and calculating the cord areas can be summarised as follows:
- Load an axial (transverse) image containing an MRI cord scan
into Jim's display. You can use Cord Finder with either
T1- or T2-weighted
images. If your images are not axial, you will need to reformat them to approximately axial
orientation using either the Image Resampler or
Multi-Planar Reconstruction tools.
- Mark the centre of the spinal cord on your desired range of slices using the
ROI Toolkit.
- Automatically outline the cord, and review the outline produced by Cord Finder.
- Calculate the areas and volume of the cord over the selected range of slices.