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- add comment paper vs. retrained weights.
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dkuegler committed Jun 20, 2024
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Expand Up @@ -13,12 +13,14 @@ Hypothalamic subfields segmentation pipeline
* EUDAT (FZ Jülich) data repository: https://b2share.fz-juelich.de/records/2af6da63d5c1414b832c1f606bbd068a
* Zenodo data repository: https://zenodo.org/records/11184216

Note: These weights (version 1.1) are retrained compared to paper ([version 1.0](https://b2share.fz-juelich.de/records/27ab0a28c11741558679c819d608f1e7)) for better rotation generalization, performance is equivalent.

### Pipeline Steps
1. Registration (optional, only required for multi-modal input)
2. Hypothalamus Segmentation

### Running the tool
- The HypVINN output can be obtained by running the default `run_fastsurfer.sh` script (for more information see [Fastsurfer documentation](../README.md)).
- The HypVINN output can be obtained by running the default `run_fastsurfer.sh` script (for more information see [FastSurfer documentation](../README.md)).
- HypVINN can also be run independently by running `HypVINN/run_prediction.py`, however we recommend running the whole FastSurfer pipeline as it includes all the required pre-processing steps.
- HypVINN has the following arguments:
### Input and output arguments
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