Comments (3)
Hi,
strange. That should not happen.
What is stored in data and what is stored in seg? Can you please run np.unique(data_dict['seg'])? Can you also try to set order_seg=0 in the SpatialTransform?
Best,
Fabian
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Hi,
strange. That should not happen.
What is stored in data and what is stored in seg? Can you please run np.unique(data_dict['seg'])? Can you also try to set order_seg=0 in the SpatialTransform?
Best,
Fabian
Hi, FabianIsensee
First of all, thank you very much for your answer. After I set order_seg = 0, it really worked and very fast. The following is the result after run np.unique(batch['seg']). Unlike the brats2017, the 'seg' here is a value that varies continuously from 0 to 1. Why change the order_seg, I am still unclear. Will changing the order_seg have other effects? Thanks!
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Thanks!
I looks like you made a mistake in resampling the segmentation. After your resampling it seems like seg is not anymore a segmentation map (discrete values) but has now continuous values. batchgenerators resamples segmentations properly (to avoid interpolation artifacts) and thus needs to process each label (i.e. each unique value) separately. If you plug a float map into the 'seg' key then this is going to take ages because there are MANY unique values. If I remember correctly, ISLES has only 2 labels (0=background, 1=lesion), so in your case you can just np.round seg and the problem goes away :-)
Best,
Fabian
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