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Merge pull request #2 from phcerdan/fix_readme
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Fix Readme typo
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ejulrich authored Oct 27, 2023
2 parents 9fa58b6 + 4e9dbf1 commit c9c4686
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9 changes: 6 additions & 3 deletions README.md
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Expand Up @@ -34,14 +34,17 @@ python -m mdai_utils.upload_annotation_slice \

## Upload 3D segmentations

MDai works with dicoms, and use the SOPInstanceUID as the key to match slices.
Your algorithm might work with 3D volumes, (.nrrd, .nii.gz, etc). You can convert the an input dicom_folder to a 3D volume, and also store the mapping between the new volume indices and the original dicom file, with its SOPInstanceUID.
MD.ai works with dicoms, and use the SOPInstanceUID as the key to match slices.
Your algorithm might work with 3D volumes, (.nrrd, .nii.gz, etc). You can convert
an input dicom_folder to a 3D volume, and also store the mapping between the new
volume indices and the original dicom file, with its SOPInstanceUID.

```bash
python -m mdai_utils.dicom_to_volume -i ./tests/fixtures/humanct_0002_1000_1004 -o /tmp/humanct_0002_1000_1004.nrrd
```

Parallel to the output image location, a `{image_filename}_SOPInstanceUIDs.json` will be saved with the slice
Parallel to the output image location, a `{image_filename}_SOPInstanceUIDs.json`
will be saved with the slice
mappings.

If we have a 3D volume segmentation we want to upload, use the mappings:
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