How can I get the trackings from the bundle masks that are predicted from my model?

[luqily]

Hi, I am sorry to bother you again.
I have gotten the bundle masks from my own model. And how can I get the trackings from them?

[wasserth]

Just look into the documentation. There is a detailed description. It's not difficult: https://github.com/MIC-DKFZ/TractSeg#create-bundle-specific-tractograms

[luqily]

Just look into the documentation. There is a detailed description. It's not difficult: https://github.com/MIC-DKFZ/TractSeg#create-bundle-specific-tractograms

Thanks for your reply.
But I only have trained the model for tract_segmentation. I don't have endings_segmentation and TOM. Can I use this to get the trackings?

[wasserth]

If you want to run with your own training data, you have to retrain your model for those as well. This is a bit more complicated because you first have to preprocess the training streamlines to get endings masks and peak maps for training.
For endings segmentations see this code: tractseg/tractseg/libs/create_endpoints_mask_with_clustering.py.
For peaks maps see this issue: #82

[luqily]

If you want to run with your own training data, you have to retrain your model for those as well. This is a bit more complicated because you first have to preprocess the training streamlines to get endings masks and peak maps for training.
For endings segmentations see this code: tractseg/tractseg/libs/create_endpoints_mask_with_clustering.py.
For peaks maps see this issue: #82

Thanks so much!