Cord Finder Tool - Outlining the Cord

Outlining the Cord

Now that you have a set of Markers at the cord centre-line between your two landmarks, the Cord Finder will use them to outline the spinal cord.

First, select the ROI file you created in the previous step by clicking on the select_roi_file_button button, and navigating to the ROI file. Setup the automatic cord outlining according to your needs. The following can be set to alter the quality of the cord outlining:

When selected, the position of your cord centre-line Marker ROIs will be refined using a model of the cord as described in this paper. Selecting this option is strongly recommended to improve both intra- and iter-observer reproducibility. To maintain compatibility with previous versions of Jim, leave this unchecked.
This is the (approximate) cord diameter. For human subjects, we recommend you try a setting of 8 mm. Making this smaller will bias the Cord Finder towards finding smaller cords, and vice versa.
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.
This determines how smoothly the cord shape varies in the head-foot direction. A small order will give a cord shape that varies very smoothly from slice-to-slice, while a larger number will allow a larger slice-to-slice variation. We recommend you use an order of 6 for relatively short section of cord, such as the cervical region, and only increase it for longer sections, or decrease it for very short sections of cord.
Select this if you are working with a T₂-weighted image. If working with a T₁-weighted image, then leave this unchecked.

Normally, the cord area is calculated over the same range of slices over which you place the cord centre-line Marker ROIs. However, you may wish to mark the cord centre-line over a greater range of slices than you want measure the cord area. If you have problems with the cord outline becoming unsteady at the extreme ends of the cord, you can help to prevent this by marking further along the cord that you want to measure, but then restricting the calculation of area just to a sub-set of slices. This can be particularly helpful if you are only measuring over a short section of cord. Select the range of slices over which cord outline ROIs are produced and areas calculated by inputting a slice range into the fields shown below:

If either field is empty, the slice range from the first / up to the final cord centre Markers (inclusive) is used.

For any particular study, you should use the same values of the tuneable settings for all subjects and all time points in the study. Clicking on the button will ensure that these settings are used the next time you start the Cord Finder.

Finally, click on the find_cord_button button. The Cord Finder will now start working and when finished (normally after approximately 1 minute), a set of Irregular ROIs will be added to the displayed cord image, outlining the cord on every slice between your landmarks:

cord_outline
Cord outline at the C3 level.

You should review the outlines to check for any gross errors. When you are learning to use the Cord Finder, you may need to experiment with changing the settings above to achieve a cord outline that follows the cord shape on all slices. However, these settings should be fixed when you come to study a patient cohort under trial conditions.

When you are happy with the outlines, you should go on to calculate the cord areas and volumes.

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