Morphometric measures definition

Dear SCT experts,
I have question about definiton of morphometric metrics/measures for diagnosis of SC compression:

In the paper Martin et al., 2018 (full ref below) are described 3 morphometric metrics/measures:

  1. Flattening - measured with compression ratio (CR)=AP/transverse diameter
  2. Indentation - measured using solidity=the percentage of area representing spinal cord within the convex hull that subtends the spinal cord
  3. Torsion - measured with relative rotation, which was calculated as the angle between the transverse axis and horizontal, relative to adjacent slices (difference from the average rotation of above and below slices)

I would like to ask how are these metrics related with metrics extracted by sct_process_segmentation function (respectively by function which is called by it) (I use SCT v4.0.0). I can get following morphometric measures from this function:

  1. Area
  2. Angle_AP, angle_RL
  3. Diameter_AP, diameter_RL
  4. Eccentricity
  5. Orientation
  6. Solidity

It is clear that from diameter_AP and diameter_RL I can compute CR which represents Flattening how is it defined in Martin et al., 2018 paper.

But I am not sure which outputs from sct_process_segmentation function (If any) are analogical to Indentation and Torsion from Martin et al.,2018 paper. Could you please clarify to me if there is relationship between metrics from the paper and from sct_process_segmentation function?

Maybe, second question. I know that SCT is under continuous development and I can see in file at github that sct_process_segmentation function has been little bit modified between v4.0.0 and current v4.1.0. Should I recompute morphometric metrics again with this newest SCT version?

Thanks a lot!
Jan Valošek


Martin, A. R., De Leener, B., Cohen-Adad, J., Cadotte, D. W., Nouri, A., Wilson, J. R., … Fehlings, M. G. (2018). Can microstructural MRI detect subclinical tissue injury in subjects with asymptomatic cervical spinal cord compression? A prospective cohort study. BMJ Open, 8(4), e019809.

Hi @valosekj,

Thank you for reaching out. As you rightly pointed out, the ratio of diameter_AP/diameter_RL would give you the flattening. Please note that these diameters correspond to the major and minor axis of the estimated ellipse (fitted to the spinal cord, slicewise). The term “AP” and “RL” refer to the axes which are mostly aligned with AP and RL respectively.

Based on Martin et al., the indentation would be represented by the solidity, and the torsion by the orientation.

Regarding your second question, yes, I would suggest to calculate the metrics again with the latest version.


Thank you, Julien!
I had similar idea about solidity and orientation but based on the little bit different definition in the paper and in the sct_process_segmentation function I was not sure, thanks for clarifying!


Dear Julien,
I and one my colleague have still some doubts about Torsion computation. In the mentioned Martin et al., 2018 paper is written: “Torsion was measured with relative rotation, which was calculated as the angle between the transverse axis and horizontal, relative to adjacent slices (difference from the average rotation of above and below slices)”. However, sct_process_segmentation function returns orientation and not relative rotation . Is our assumption correct that relative rotation (how is defined in Martin, 2018 paper) can be computed from the orientation (obtained from sct_process_segmentation) in one slice and two adjacent slices? If so, could you please provide us formula for computation?

Thanks a lot,

Dear Jan,
yes you are absolutely right. There are different ways to compute the “relative” torsion (e.g., how many adjacent slices you consider, how you weight them, etc.) so it is difficult for me to provide the “right” answer.

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