Semi-Automatic Cord Outlining

For semi-automatic cord outlining, ensure that the Checkbox for quasi-automatic processing not selected checkbox is not selected.

Reformatting to Axial (Transverse) Orientation

In semi-automatic mode, the Cord Finder tool will only work with images that are in an approximately axial (transverse) orientation, with the cord seen in cross-section running through the slices. If your images are not axial (transverse) because, for example, they were acquired using a 3-D pulse sequence, you can use Jim to reformat them to axial. You can do this using either the Image Resampler or the Multi-Planar Reconstruction tool. Below, we describe how to do this for a section of the cervical cord, using Multi-Planar Reconstruction. With the Cord Finder in semi-automatic mode, you are not restricted to just analysing the cervical region, but we use this for illustrative purposes.

Load the image to be analysed into Jim's main display, then launch the Multi-Planar Reconstruction. Adjust the sample volume in the Multi-Planar Reconstruction display so that:

  1. In the upper-left quadrant, position the centre handle near to the centre of the cord.
  2. In the upper-right quadrant, position the centre handle close to the centre of the cord at the C2/C3 disk so that whole of cord from cerebellum to the inferior extent of the cord can be seen. Extend the resampling box in the S/I direction as necessary.
  3. In the upper-right quadrant use the rotation handle at the right or left to rotate the sample volume so that the edges are parallel to the cord at the C2/C3 disk. If you are interested in measuring the cord area at a particular location, then make the edges of the sample volume parallel to the cord at that location, rather than at the C2/C3 disk.
  4. In the bottom left quadrant, ensure that the whole of the cord is within the field of view in the left-right direction by adjusting the field of view if necessary.

cord_mpr

In the Multi-Planar Reconstruction dialog, ensure that the Interpolation type is set to "Sinc" and that "Save to disk" is selected. Then click the Button to do the multi-planar reconstruction resampling button in the Multi-planar reconstruction dialog. This will bring up a File Chooser for you to save the resampled image with a new name.

Marking the Cord

Now that you have a set of axial (transverse) slices, you can go on to manually mark the approximate centre line of the cord. You need to select two landmarks along the cord so that you reliably identify the section of cord you are to assess. In this example, we will be evaluating the cord cross-sectional area between the superior margin of C2 and the disk at the C5/C6 level.

First load the axial image into Jim's main display. Then from "View" menu, select "Ortho views": view_ortho_views

Use the orthogonal views to identify the most superior slice in which the odontoid process of the epistropheus (C2) is still just visible (as shown arrowed in the picture below).

cord_odontoid
Most superior slice with the odontoid process just still visible,
with the first cord centroid Marker.

Place a Marker ROI at the centre-of-area of the cord. When placing a Marker, please ensure that:

  1. The main display of the axial slice is well zoomed in so that you can place the Marker accurately at the centre of the cord.
  2. You take care in this interactive part of the analysis. Place the Marker on the mid-line and mid-way between the most anterior and most posterior portions of the cord.

Now move down through the slices to the C5/C6 disk and place a marker at the centre-of-area of the cord there. Use the inferior border of C5 as a reference, as shown in the picture of the orthogonal view below. Place a Marker approximately every 10 mm (every 10 slices for a slice thickness of 1 mm), and be sure to place a final Marker on the last slice where you identify your second landmark.

cord_c5_c6

Save the ROIs to a disk file. This ROI file will be used to outline the cord, as shown below..

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 Button for selecting the cord centre-line ROI file button, and navigating to the ROI file. Setup the automatic cord outlining according to your requirements. The following can be set to alter the quality of the cord outlining:

  • Check box to refine the cord centre-line 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 inter-observer reproducibility. To maintain compatibility with previous versions of Jim, leave this unchecked.

  • cord_nominal_diameter 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.

  • 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 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.

  • cord_order 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.

  • Cord is hypointense check box 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:

    Selecting the first and last slices for cord area calculation

    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 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 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 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.

Cord Areas and Volume

Now that you have outlined the cord between your two landmarks, you can calculate the cross-sectional areas along the cord, and the total cord volume.

First, select the whether you want to:

  • Check box to generate a straightened cord image. This produces an image that aids visualisation of the cord and its pathology, but is not needed for quantification. The cord centre-line is straightened, and a new image is created with scan planes that are now perpendicular to the cord centre-line. An example unfolded image is shown below for the cervical cord, seen in orthogonal views.

    A view of the straightened cervical spinal cord
    Straightened cervical cord image in coronal (left) and sagittal (right) views.

    The straightened cord image will take its name from the input image, but with a suffix "Cord" added.

    Note: normally, in the straightened cord image, the pixel size (pixel width and pixel height) and field of view in the left-right and anterior-posterior directions will be half that of the input image. If you use a heavily cropped input image (cropped close to the cord in the left-right or anterior-posterior directions), the straightened cord image may not contain the whole of the spinal cord. In which case, you can create an image with the original field-of-view and pixel sizes by selecting the Check-box to give a straightened image with the full fov check-box.

  • cord_vrml_check. With this selected, a surface model of the cord will be created, which can then be loaded into the 3-D Display as a virtual reality modelling language (VRML) file. The VRML file created will have a name taken from the input image name, with an extension .wrl. An example is shown below, with the VRML cord surface shown as a mesh against a background of the cord image in orthogonal views.

cord_vrml
Surface mesh of cervical cord.

Now click on the calculate_button button. When the calculation is finished, a dialog will pop up, showing the cord cross-sectional area and volume between the landmarks.

Dialog showing the results of the Cord Finder

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 equal to the original slice thickness) 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 most superior and most inferior landmarks also pops up:

Popup showning the cross-sectional area of the cord between the superior and inferior landmarks.