sct_compute_compression

Compute normalized morphometric metrics to assess:

  • spinal cord compression using MSCC (maximum spinal cord compression)

  • spinal canal stenosis using MCC (maximum canal compromise)

Metrics are normalized using the non-compressed levels above and below the compression site (or injury site with lesion) using the following equation:

ratio = (1 - mi/((ma+mb)/2))

Where mi: metric at the compression level, ma: metric above the compression level, mb: metric below the compression level.

Additionally, if the -normalize-hc flag is used, metrics are normalized using a database built from healthy control subjects. This database uses the PAM50 template as an anatomical reference system.

References:

  • Sandrine Bédard, Jan Valošek, Maryam Seif, Armin Curt, Simon Schading, Nikolai Pfender, Patrick Freund, Markus Hupp, Julien Cohen-Adad. Normalizing Spinal Cord Compression Morphometric Measures: Application in Degenerative Cervical Myelopathy. medRxiv 2024.03.13.24304177 https://doi.org/10.1101/2024.03.13.24304177

  • Miyanji F, Furlan JC, Aarabi B, Arnold PM, Fehlings MG. Acute cervical traumatic spinal cord injury: MR imaging findings correlated with neurologic outcome–prospective study with 100 consecutive patients. Radiology 2007;243[3]:820-827. https://doi.org/10.1148/radiol.2433060583

  • -normalize-hc flag: Valošek J, Bédard S, Keřkovský M, Rohan T, Cohen-Adad J. A database of the healthy human spinal cord morphometry in the PAM50 template space. Imaging Neuroscience 2024; 2 1–15. https://doi.org/10.1162/imag_a_00075

usage: sct_compute_compression -i <file> -l <file> [-vertfile <file>]
                               [-mode {compression,lesion}] [-extent <float>]
                               [-distance <float>] [-o <file>]
                               [-normalize-hc <int>]
                               [-metric {diameter_AP,area,diameter_RL,eccentricity,solidity}]
                               [-sex {F,M}] [-age [0 100] [0 100]] [-h]
                               [-v <int>]

MANDATORY ARGUMENTS

-i

Spinal cord or spinal canal segmentation mask to compute morphometrics from. If spinal cord segmentation is provided, MSCC is computed. If spinal canal segmentation (spinal cord + CSF) is provided, MCC is computed. Example: sub-001_T2w_seg.nii.gz

Note: If no normalization is wanted (i.e., if the -normalize-hc flag is not specified), metric ratio will take the average along the segmentation centerline.

-l

A NIfTI file that includes either i) compression labels or ii) lesion mask. i) compression labels = labels at the compression sites. Each compression site is denoted by a single voxel of value 1. Example: sub-001_T2w_compression_labels.nii.gz. Use the -mode compression flag when providing this input. ii) lesion mask = binary mask of the lesion. Currently only a single lesion is supported. Example: sub-001_T2w_lesion.nii.gz. Use the -mode lesion flag when providing this input.

Note: The ‘-i’ and ‘-l’ files must be in the same voxel coordinate system and must match the dimensions between each other.

OPTIONAL ARGUMENTS

-vertfile

Vertebral labeling file. Example: sub-001_T2w_seg_labeled.nii.gz

Note: The ‘-i’ and ‘-vertfile’ files must be in the same voxel coordinate system and must match the dimensions between each other.

-mode

Possible choices: compression, lesion

Choose between:

  • compression: use compression labels (provided by the ‘-l’ arg).

  • lesion: use lesion mask (provided by the ‘-l’ arg). In this case, the level of maximum injury is automatically determined as the axial slice within the lesion mask that has the minimum spinal cord AP diameter.

Default: 'compression'

-extent

Extent (in mm) to average metrics of healthy levels in superior-inferior direction.

Default: 20.0

-distance

Distance (in mm) in the superior-inferior direction from the compression to average healthy slices.

Default: 10.0

-o

Output CSV file name. If not provided, the suffix _compression_metrics is added to the file name provided by the flag -i.

NORMALIZATION ARGUMENTS

-normalize-hc

Possible choices: 0, 1

Set to 1 to normalize the metrics using a database of healthy controls. Default: 0.

Note: This flag should not be set to 1 when computing the MCC (i.e. using spinal canal segmentation), and should only be used when computing the MSCC (i.e. using spinal cord segmentation).

-metric

Possible choices: diameter_AP, area, diameter_RL, eccentricity, solidity

Metric to normalize.

Default: 'diameter_AP'

-sex

Possible choices: F, M

Sex of healthy subject to use for the normalization. By default, both sexes are used.

-age

Age range of healthy subjects to use for the normalization. Example: -age 60 80. By default, all ages are considered.

MISC ARGUMENTS

-v

Possible choices: 0, 1, 2

Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode.

Default: 1