sct_deepseg¶

Here we provide a gallery of each model available in the sct_deepseg CLI tool.

Spinal cord¶

Spinal cord segmentation can be performed by running the following sample command:

sct_deepseg spinalcord -i input.nii.gz

You can replace “spinalcord” with any of the task names in the table below to perform different tasks. Click on a task below for more information.

`spinalcord`	`sc_lumbar_t2`	`sc_epi`
`sc_mouse_t1`

Gray matter¶

Gray matter segmentation can be performed by running the following sample command:

sct_deepseg graymatter -i input.nii.gz

You can replace “graymatter” with any of the task names in the table below to perform different tasks. Click on a task below for more information.

`graymatter`	`gm_sc_7t_t2star`	`gm_wm_exvivo_t2`
`gm_wm_mouse_t1`	`gm_mouse_t1`

Pathologies¶

Pathology segmentation can be performed by running the following sample command:

sct_deepseg lesion_sci_t2 -i input.nii.gz

You can replace “lesion_sci_t2” with any of the task names in the table below to perform different tasks. Click on a task below for more information.

`lesion_sci_t2`	`lesion_ms`	`lesion_ms_axial_t2`
`lesion_ms_mp2rage`	`tumor_edema_cavity_t1_t2`	`tumor_t2`

Other structures¶

Multiple structures may be segmented by running the following sample command:

sct_deepseg rootlets -i input.nii.gz

You can replace “rootlets” with any of the task names in the table below to perform different tasks. Click on a task below for more information.

rootlets

totalspineseg

sc_canal_t2

Retired models¶

These models have been replaced by newer, more advanced models. We recommend switching to the model listed in the table below.

If you absolutely require these models, you can downgrade to version of SCT listed in the table below. If you do this, please let us know on the SCT Forum so we can better understand your use-case, and potentially reinstate the model if necessary.

Model	Last available	Superseded by
`seg_sc_ms_lesion_stir_psir`	SCT Version `6.4`	`lesion_ms` (contrast-agnostic MS lesion segmentation)
`ms_sc_mp2rage`	SCT Version `6.4`	`spinalcord` (contrast-agnostic SC segmentation)
`sc_t2star`	SCT Version `6.5`	`spinalcord` (contrast-agnostic SC segmentation) and `sc_epi` (for EPI-BOLD fMRI SC segmentation)