Contrast-agnostic-spinal-cord-v3.0 (r20250402)

SCT
1

Dear SCT Team,
I noticed from your [v3.0 release ] (Release contrast-agnostic-spinal-cord-v3.0 (r20250402) · sct-pipeline/contrast-agnostic-softseg-spinalcord · GitHub) that the deepseg contrast-agnostic models have been upgraded. I have downloaded the latest model (model_contrast_agnostic_20250123) and saved it in the sct_6.5/data/deepseg_models folder. However, when I run
“sct_deepseg -task seg_sc_contrast_agnostic -i < my_input_file>”
it installs and runs model_seg_sc_contrast_agnostic_softseg_monai, which appears to be version 2.5. I am running my analysis on compressed spinal cord data, and it looks like version 3.0 works especially well with compressed cords. How can I ensure that my batch analysis uses the updated deepseg version 3.0? Could you please advise on the correct command or configuration to run version 3.0?
Thank you for your assistance.
Fauziyya

3

Hi SCT Team, I found the correct link for the installation. Thank you!

4

Dear @Mfauziyya,

My apologies for the late reply. I am responding just to clarify a few things:

  • Version 3.0 is the latest release of the model, and is planned to be released formally in SCT v7.0, which will be released in a few weeks.
  • To explain the behavior you encountered for version 2.5 / SCT v6.5: SCT will try to keep the model version and SCT version in sync. So, even though you manually downloaded v3.0, SCT will try to revert back to v2.5, since that is the version that was released with SCT v6.5.
  • If you want to bypass the behavior, you can use the -custom-url flag. This flag will take care of downloading and extracting the model files for you, and it will also bypass the mechanism used to keep the existing v2.5 version.
sct_deepseg -task seg-sc-contrast-agnostic -install -custom-url https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/releases/download/v3.0/model_contrast_agnostic_20250123.zip

Apologies for the confusion, and thanks for your understanding.

Kind regards,
Joshua

5

Hi Joshua,
Thank you for your guidance. I ran the command you suggested, and the v3.0 model installed successfully.
Below is a section of the log:
Trying URL: https://github.com/sct-pipeline/contrast-agnostic-softseg-spinalcord/releases/download/v3.0/model_contrast_agnostic_20250123.zip

Downloading: model_contrast_agnostic_20250123.zip
Creating temporary folder (/var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2025-04-17_14-41-44_install-data_qy33ikhb)

Unzip data to: /var/folders/9y/fz81lr6n7yx98800mstcqgb80000gp/T/sct_2025-04-17_14-41-44_install-data_qy33ikhb

Copying data to: /Users/FMUHAMMA/sct_6.5/data/deepseg_models/model_seg_sc_contrast_agnostic_softseg_monai

Removing temporary folders…

Thanks,
Fauziyya