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--- |
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language: |
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- en |
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pipeline_tag: image-segmentation |
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tags: |
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- medical |
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library_name: fastMONAI |
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--- |
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# Multi-Center CNN-based spine segmentation from T2w MRI using small amounts of data |
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Pre-trained weights and exported models for our spine segmentation project. |
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The source code, designed to reproduce our test results and facilitate training and running inference on your own data, is available on GitHub: https://github.com/MMIV-ML/fastMONAI/tree/master/research |
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## Requirements |
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Last checked and validated with fastMONAI version 0.3.2. Please ensure that you have the correct version of fastMONAI installed to guarantee the correct operation of the model. |
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## Data |
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### Haukeland University Hospital (HUH): 15 T2-weighted MRI scans |
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- [Study](https://trialsjournal.biomedcentral.com/articles/10.1186/s13063-017-2306-8) |
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#### Scanner Specifications |
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- Type: Siemens MAGNETOM Avanto 1.5 T |
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- Slice Thickness: 4 mm |
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- Field of View (FOV): 300x300 mm^2 |
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- Matrix: 384x269 |
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- Interslice Gap: 0.4 mm |
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- Repetition Time: 3700 ms |
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- Echo Time: 87 ms |
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- Number of Acquisitions: 2 |
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### Sahlgren-ska University Hospital (SUH): 10 T2-weighted MRI scans |
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- [Study](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789539/) |
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#### Scanner Specifications |
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- Type: Siemens MAGNETOM Aera 1.5 T |
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- Slice Thickness: 3.5 mm |
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- Field of View (FOV): 300x300 mm^2 |
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- Matrix: 384x384 |
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- Interslice Gap: 0.7 mm |
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- Repetition Time: 3500 ms |
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- Echo Time: 95 ms |
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- Number of Acquisitions: 1 |
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### Data Annotation |
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- **Process**: Manual segmentation of vertebrae |
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- **Experts**: Conducted by an MRI expert with consensus from a senior radiologist |
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- **Software**: ITK-SNAP |
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- **Scope**: Segmented vertebrae in all slices, including bone marrow but excluding vertebral cortex |
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### External Data Evaluation |
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- **Source**: [Annotated T2-weighted MR images of the Lower Spine](https://zenodo.org/record/22304) |
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- **Scan Specifications**: 23 scans, 1.5 T in sagittal orientation |
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- **Segments**: Seven vertebrae are manually segmented on each image (Th11–L5) |
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- **Modification**: Th11 manually removed for consistency with the annotation for SUH and HUH. |
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