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README.md
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@@ -14,4 +14,49 @@ The source code, designed to reproduce our test results and facilitate training
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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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## 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 Collection
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### Origin of MRI Scans
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- **Haukeland University Hospital (HUH)**: 15 T2-weighted MRI scans
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- **Sahlgren-ska University Hospital (SUH)**: 10 T2-weighted MRI scans
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### HUH Data
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- **Study**: [AIM-study (Antibiotics In Modic changes)](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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### SUH Data
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- [Link to Sahlgrenska Data](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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