model_seg_ms_mp2rage

Model repository for MS lesion segmentation on MP2RAGE data (UNIT1 contrast)

Model overview

3D model trained with nnUNetv2 framework.

Dependencies

SCT 6.4

Datasets for training

• basel-mp2rage
• nih-ms-mp2rage
• marseille-3t-mp2rage

Installation

sct_deepseg -install-task seg_sc_contrast_agnostic

sct_deepseg -install-task seg_ms_lesion_mp2rage 

Warning: When running the MS lesion segmentation model, the image first need to be cropped around the spinal cord mask with a dilation of 30 mm in the axial plane and 5 mm in the Z-axis.

Launch MS lesion segmentation:

1. Spinal cord segmentation

   sct_deepseg -i IMAGE_UNIT1 -task seg_sc_contrast_agnostic -o IMAGE_UNIT1_sc

2. Cropping with dilation (for axial orientation images with 1mm isotropic resolution)

   sct_crop_image -i IMAGE_UNIT1 -m IMAGE_UNIT1_sc -dilate 30x30x5 -o IMAGE_UNIT1_cropped

3. MS lesion segmentation

   sct_deepseg -i IMAGE_UNIT1_cropped -task seg_ms_lesion_mp2rage 

Model implementation on Slicer

1. Install 3D Slicer version 5.7.0, then install the module SlicerNNUnet from the extensions explorer.

2. Download and unzip the nnUNetTrainer_seg_ms_lesion_mp2ragennUNetPlans3d_fullres.zip file. (~120 Mb)

3. Unzip the .zip file and place it inside a folder named Dataset403_seg_ms_lesion_mp2rage_1mm_322subj. The final directory structure should look like this:

   Dataset403_seg_ms_lesion_mp2rage_1mm_322subj
   └── nnUNetTrainer_seg_ms_lesion_mp2rage__nnUNetPlans__3d_fullres
   ├── dataset_fingerprint.json
   ├── dataset.json
   ├── dataset_split.md
   ├── datasplits
   │   ├── datasplit_basel-mp2rage.yaml
   │   ├── datasplit_marseille-3t-mp2rage.yaml
   │   └── datasplit_nih-ms-mp2rage.yaml
   ├── fold_3
   │   ├── checkpoint_final.pth
   │   ├── debug.json
   │   ├── progress.png
   │   └── training_log_2024_3_14_20_35_08.txt
   └── plans.json

4. nnUNet Install: Follow the instructions on first row of:

5. Implementation

   • Navigate and select the Slicer friendly folder on Model path
   • Folds: Choose the fold 3
   • Apply model_seg_ms_mp2rage !! 🚀🚀🚀

Acknowledgments

• Charidimos Tsagkas (Translational Neuroradiology Section, National Institutes of Health, Bethesda, USA)
• Daniel Reich (Translational Neuroradiology Section, National Institutes of Health, Bethesda, USA)
• Cristina Granziera (Neurologic Clinic and Policlinic, University Hospital Basel and University of Basel, Basel, Switzerland)
• Virginie Callot (Center for Magnetic Resonance in Biology and Medicine, CRMBM-CEMEREM, UMR 7339, CNRS, Aix-Marseille University, Marseille, France)