Quasi-Automatic Cord Outlining

The quasi-automatic Cord Finder can outline the cord almost automatically on a T1-weighted MRI scan of the cervical region. For quasi-automatic cord outlining, ensure that the Checkbox for quasi-automatic processing selected checkbox is selected. Then the Cord Finder tool changes to look like this:

The Cord Finder tool in quasi-automatic mode

Image to be Analysed

Load the T1-weighted image into Jim's main display. The image can be in any orientation (axial/sagittal/coronal), but should cover at least the region approximately from the base of the cerebellum to the lowest landmark at which you want to assess the cord.

Placing the C2/C3 Disk Landmark

In order to detect all cord landmarks reliably, you must manually identify the position of the inter-vertebral disk between C2 and C3 by placing a Marker ROI just anterior to the cord at this location.

The picture below shows the correct positioning of this Marker on a sagittal image, together with the (axial and coronal) orthogonal views.

Marking the C2/C3 disk on a sagittal view for quasi-automatic processing

C2/C3 marker position on a sagittal cervical cord image

The Marker on the mid-line, is anterior to the cord and at the posterior tip of the disk.

The picture below shows the correct positioning of a Marker on an axial image, together with the (coronal and sagittal) orthogonal views.

Marking the C2/C3 disk on an axial view for quasi-automatic processing

C2/C3 marker position on an axial cervical cord image

Save the Marker ROI into an ROI file. The ROI file must have a base name which is the same as the image to be analysed. For example, if you are analysing an image called SpinalCord.nii.gz, the ROI file must be called SpinalCord.roi.

Selecting the Cord Analysis Extent

Now set the extent of the cord over which you want to assess cross-sectional area.

Panel for selecting the cord analysis region.

Select the most superior landmark in the "First landmark" panel, and the most inferior landmark in the "Final landmark" panel. You can select any pair of landmarks between the odontoid process of the epistropheus (OPE) and the T4/T5 disk. However, if these anatomical landmarks are not present in the image because they are outside the field-of-view, then you will see an error message part way through processing.

If you select the same landmark in both the "First landmark" and "Final landmark" panels, then the panel below is shown for you to set the thickness of a slab of slices centred on that landmark.

Panel for selecting slab thickness for cord outlining.

You can set the slab thickness between 1 and 41 mm, in steps of 2 mm, which is positioned so that the cord assessment landmark is always in the central slice of the slab.

Outlining the Cord

Finally, set the cord_n_coeffs 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 between 8 and 16 coefficients, with the lower value used when the images have poor contrast-to-noise ratio. Increase it when the outlines produced are excessively smooth and do not follow the cord shape accurately in all slices.

For any particular study, you should use the same value for all subjects and all time points in the study. Clicking on the save_settings_button 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 quasi-automatic Cord Finder will now start working and when finished (normally after several minutes) the following pops up:

Popup showning the results of the quasi-automatic cord analysis.

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.

A report will detail the cord length, total volume and cross-sectional areas at regular intervals (in steps of 1 mm) down the cord. The cross-sectional areas are measured in a plane that is perpendicular to the local cord centre-line.

A plot of the cord cross-sectional area between the superior and inferior landmarks also pops up:

Popup showning the cross-sectional area of the cord between the 2 landmarks.

For an input image called "CordImage.nii", the following outputs will be produced:

  • CordImage_Cord.nii - a straightened cord image with slices that are in the axial plane.
  • CordImage_CordLandmarks.roi - an ROI file containing Markers at all the cord landmarks from OPE to T4/T5 that are within the field-of-view. These can be viewed by loading them onto the CordImage_Cord.nii image. The Markers should be at the centre of the cord, opposite the identified landmarks.
  • CordImage_Cord.roi - an ROI file containing cord outlines between the two landmarks that you selected (or over the slab that you set). These can be viewed by loading them onto the CordImage_Cord.nii image.

You should review the outlines to check for any gross errors. If you are not satisfied either with the landmark identification, or with the cord outlines produced, you can:

  • Adjust the Landmark markers. To help with identification, each of the Landmark markers is annotated with its intended location. Whilst referencing the orthogonal view, cut-and-paste the Marker into the correct slice for that location. Save the ROIs, then re-run the analysis.
  • If the Landmark ROIs are in the correct location, but the outline ROIs are incorrect, you can change the cord_n_coeffs or you can manually edit the ROI outlines and save the changes. Then run the analysis again.