| | --- |
| | language: |
| | - en |
| | pipeline_tag: image-segmentation |
| | tags: |
| | - medical |
| | library_name: fastMONAI |
| | --- |
| | # 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. |
| | 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 |
| |
|
| | ## Requirements |
| | 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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| |  |
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| | ## Data |
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| | ### Haukeland University Hospital (HUH): 15 T2-weighted MRI scans |
| | - [Study](https://trialsjournal.biomedcentral.com/articles/10.1186/s13063-017-2306-8) |
| | #### Scanner Specifications |
| | - Type: Siemens MAGNETOM Avanto 1.5 T |
| | - Slice Thickness: 4 mm |
| | - Field of View (FOV): 300x300 mm^2 |
| | - Matrix: 384x269 |
| | - Interslice Gap: 0.4 mm |
| | - Repetition Time: 3700 ms |
| | - Echo Time: 87 ms |
| | - Number of Acquisitions: 2 |
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| | ### Sahlgren-ska University Hospital (SUH): 10 T2-weighted MRI scans |
| | - [Study](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789539/) |
| | #### Scanner Specifications |
| | - Type: Siemens MAGNETOM Aera 1.5 T |
| | - Slice Thickness: 3.5 mm |
| | - Field of View (FOV): 300x300 mm^2 |
| | - Matrix: 384x384 |
| | - Interslice Gap: 0.7 mm |
| | - Repetition Time: 3500 ms |
| | - Echo Time: 95 ms |
| | - Number of Acquisitions: 1 |
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| | ### Data Annotation |
| | - **Process**: Manual segmentation of vertebrae |
| | - **Experts**: Conducted by an MRI expert with consensus from a senior radiologist |
| | - **Software**: ITK-SNAP |
| | - **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) |
| | - **Scan Specifications**: 23 scans, 1.5 T in sagittal orientation |
| | - **Segments**: Seven vertebrae are manually segmented on each image (Th11–L5) |
| | - **Modification**: Th11 manually removed for consistency with the annotation for SUH and HUH. |
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