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. The tool can be used either semi-automatically, or quasi-automatically. The semi-automatic method is described in this paper.

In addition, there is a specialised tool for estimating the change in atrophy between two time-points either (semi-automatically), or (quasi-automatically). The semi-automatic method is described in this paper.

Start the Cord Finder tool from the Toolkits menu: toolkits_cord_finder

The Cord Finder tool will now appear as shown below:

cord_finder_frame

Note that the ROI Toolkit also pops up when you start the Cord Finder.

The Cord Finder tool can operate in two modes, both of which require the user to identify feature(s) in the image:

  1. In the first, the user marks the approximate centre of the cord at regular intervals between two landmarks on an axial cord image. The program then outlines the cord between those landmarks. This mode is referred to as 'semi-automatic'.
  2. In the second, the user marks one landmark at the C2/C3 disk position, and selects which section of cord should be used to assess cord area. The image can be in any orientation and requires the user only to identify a single landmark. Thus, this mode is referred to as 'quasi-automatic', and can only be used to assess the cord in the cervical or upper thoracic region.