Nick Tustison
Nick Tustison
Nice. Thanks. So if you wanted to simply use brain extraction through the ANTsXNet tools, we could include that template in the refining of the current network. It's definitely higher...
In general, I hesitate to provide much support at all for training because it's so system-dependent. In addition, although I publicly share all my scripts, network training is currently outside...
"Aggressive data augmentation" refers to the spatial and intensity transforms used in batch_generator.py, not the number of batches. Again, the training scripts are not meant for formal distribution so I...
Sure, I could do that. I'm heading out for a run but I could put it on the GPU when I get back, as long as you wouldn't mind me...
Great. Perhaps you can send a link to my email ([email protected]) where I can download the template and mask and I'll get it started when I get back.
Okay, I updated the weights in the repo and the added variance definitely improves the results on the independent data set that I've been using.   Let me know...
Great. > A quick single image test looks like it over segments into the skull but it's certainly a really good starting point if nothing else. Yeah, again, I would...
Specifically [these lines](https://github.com/ntustison/ANTsXNetTraining/blob/main/Mouse/BrainExtraction/train_model.py#L110-L111). You shouldn't have to change ``batch_generator.py``.
yeah, i've seen that and i'm guessing it was my fault. would this be a problem @stnava if we fixed it?
Here are [some tutorials](https://gist.github.com/ntustison/12a656a5fc2f6f9c4494c88dc09c5621) for pairwise and longitudinal sets of point sets in ANTsR/ANTsPy. Go down to "Fit transform to paired points" and "Velocity flows across point sets".