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.
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.
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.
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.
Spinal Canal segmentation can be performed by running the following sample command:
sct_deepseg -task canal_t2w -i input.nii.gz
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These models have been replaced by newer, more advanced models.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Superseded by |
SCT Version |
|
|
SCT Version |
|