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 -task seg_sc_contrast_agnostic -i input.nii.gz

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

seg_sc_contrast_agnostic seg_sc_contrast_agnostic

seg_lumbar_sc_t2w seg_lumbar_sc_t2w

seg_sc_epi seg_sc_epi

mice_sc mice_sc

Gray matter

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

sct_deepseg -task seg_gm_sc_7t_t2star -i input.nii.gz

You can replace “seg_gm_sc_7t_t2star” with any of the task names in the table below to perform different tasks. Click on a task below for more information.

seg_gm_sc_7t_t2star seg_gm_sc_7t_t2star

seg_exvivo_gm_wm_t2 seg_exvivo_gm_wm_t2

seg_mouse_gm_wm_t1w seg_mouse_gm_wm_t1w

mice_gm mice_gm

Pathologies

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

sct_deepseg -task seg_sc_lesion_t2w_sci -i input.nii.gz

You can replace “seg_sc_lesion_t2w_sci” with any of the task names in the table below to perform different tasks. Click on a task below for more information.

seg_sc_lesion_t2w_sci seg_sc_lesion_t2w_sci

seg_ms_lesion seg_ms_lesion

seg_ms_lesion_mp2rage seg_ms_lesion_mp2rage

seg_tumor_edema_cavity_t1_t2 seg_tumor_edema_cavity_t1_t2

tumor_t2 tumor_t2

Other structures

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

sct_deepseg -task seg_spinal_rootlets_t2w -i input.nii.gz

You can replace “seg_spinal_rootlets_t2w” with any of the task names in the table below to perform different tasks. Click on a task below for more information.

seg_spinal_rootlets_t2w seg_spinal_rootlets_t2w

totalspineseg totalspineseg

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

sct_deepseg -task canal_t2w -i input.nii.gz

canal_t2w canal_t2w

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These models have been replaced by newer, more advanced models.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Superseded by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 seg_sc_ms_lesion_stir_psir

SCT Version 6.4

seg_ms_lesion (contrast-agnostic MS lesion segmentation)

ms_sc_mp2rage ms_sc_mp2rage

SCT Version 6.4

seg_sc_contrast_agnostic (contrast-agnostic SC segmentation)