spine

Intervertebral discs labeling and vertebrae segmentation

TotalSpineSeg is a tool for automatic instance segmentation of all vertebrae, intervertebral discs (IVDs), spinal cord, and spinal canal in MRI images. It is robust to various MRI contrasts, acquisition orientations, and resolutions. The model used in TotalSpineSeg is based on nnU-Net as the backbone for training and inference.

Reference

Project URL: https://github.com/neuropoly/totalspineseg

usage: sct_deepseg spine [-i <file> [<file> ...]] [-o <str>] [-install]
                         [-custom-url CUSTOM_URL [CUSTOM_URL ...]]
                         [-largest {0,1}] [-fill-holes {0,1}]
                         [-remove-small REMOVE_SMALL [REMOVE_SMALL ...]]
                         [-qc <folder>] [-qc-dataset <str>] [-qc-subject <str>]
                         [-qc-seg <file>] [-h] [-v <int>] [-r {0,1}]
                         [-label-vert {0,1}]

INPUT/OUTPUT

-i

Image filename(s) to segment. If segmenting multiple files, separate filenames with a space.

-o

Output file name. The chosen filename will be used as a base name, and model-specific suffixes will be added to the end depending on the type of output (e.g. ‘_cord.nii.gz’, ‘_gm.nii.gz’, etc.).

TASKS

-install

Install models that are required for specified task.

Default: False

-custom-url

URL(s) pointing to the .zip asset for a model release. This option can be used with -install to install a specific version of a model. To use this option, navigate to the ‘Releases’ page of the model, find release you wish to install, and right-click + copy the URL of the .zip listed under ‘Assets’. Example: sct_deepseg spine -install -custom-url CUSTOM_URL sct_deepseg spine -i t2.nii.gz

PARAMETERS

-largest

Possible choices: 0, 1

Keep the largest connected object from each output segmentation; if not set, all objects are kept.

Default: 0

-fill-holes

Possible choices: 0, 1

If set, small holes in the segmentation will be filled in automatically.

Default: 0

-remove-small

Minimal object size to keep with unit (mm3 or vox). A single value can be provided or one value per prediction class. Single value example: 1mm3, 5vox. Multiple values example: 10 20 10vox (remove objects smaller than 10 voxels for class 1 and 3, and smaller than 20 voxels for class 2).

-label-vert

Possible choices: 0, 1

If set to ‘1’, run a second model that applies a unique label to each individual vertebrae in the spine segmentation (e.g. C1: 11 C2: 12 etc.). If not specified, all segmented vertebrae will have the same value (50), which is faster to compute if you only need e.g. disc labels. More details on TotalSpineSeg’s two models can be found here: https://github.com/neuropoly/totalspineseg/?tab=readme-ov-file#model-description

Default: 0

MISC ARGUMENTS

-qc

The path where the quality control generated content will be saved.

-qc-dataset

If provided, this string will be mentioned in the QC report as the dataset the process was run on.

-qc-subject

If provided, this string will be mentioned in the QC report as the subject the process was run on.

-qc-seg

Segmentation file to use for cropping the QC. This option is useful when you want to QC a region that is different from the output segmentation. For example, it might be useful to provide a dilated cord segmentation to expand the QC field of view.

-v

Possible choices: 0, 1, 2

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

Default: 1

-r

Possible choices: 0, 1

Remove temporary files.

Default: 1