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MIC-DKFZ / batchgenerators

A framework for data augmentation for 2D and 3D image classification and segmentation
Apache License 2.0
1.09k stars 221 forks source link

Using batchgenerators with TractSeg #27

Closed ilyanelken closed 5 years ago

ilyanelken commented 5 years ago

Hi,

I am trying to run TractSeg training, and not sure about batchgenerators version I should use. I have tried the master and got 'PadToMultipleTransform' missing. I have also tried 'tractseg_stable' branch and there I get 'FlipVectorAxisTransform' that is missing.

I will appreciate your help.

Thanks, Ilya

FabianIsensee commented 5 years ago

Hi, I renamed them a while back because the names were pretty bad. You couldn't understand what they were really doing. @wasserth should update Tractseg to use the new (more intuitive) names :-) Best, Fabian

ilyanelken commented 5 years ago

I see. Thanks! Ilya

wasserth commented 5 years ago

@ilyanelken The current master of TractSeg should work properly with current master of batchgenerators.

ilyanelken commented 5 years ago

@wasserth Great! Thanks a lot for help and update! Ilya

wasserth commented 5 years ago

@ilyanelken I just tried running TractSeg with the newest version of batchgenerators. There was a small problem but it is fixed now. So using the latest master branch should work now. Another side note: The documentation for training your own model is not completely up to date anymore. I will try to update it today or tomorrow.

wasserth commented 5 years ago

@ilyanelken There still seem to be some problems with the latest batchgenerators master. So I would recommend using the following commit: 802e9cbd556b9ebc1300beded7c10a37ef09b7b9 This should work best.

ilyanelken commented 5 years ago

@wasserth Ok! Thanks Jacob!