LiTS Dataset

Hello! I have created a .h5 file with the LiTS Dataset with shape (140, 2, 128, 128, 128), with 140 volumes, 2 labels, a scan and a mask for each, 128 slices, and 128x128 px size. I adjusted the header of the train_isensee2017.py file acordingly. When I try to run it I get the error bellow when running the get_training_and_validation_generators() function. What could it be? Thanks in advanced!

Traceback (most recent call last):
  File "/home/albaroz/PycharmProjects/tese/3DUnetCNN-master/brats/train_isensee2017.py", line 105, in <module>
    main(overwrite=config["overwrite"])
  File "/home/albaroz/PycharmProjects/tese/3DUnetCNN-master/brats/train_isensee2017.py", line 101, in main
    augment_distortion_factor=config["distort"])
  File "/home/albaroz/PycharmProjects/tese/3DUnetCNN-master/unet3d/generator.py", line 57, in get_training_and_validation_generators
    validation_file=validation_keys_file)
  File "/home/albaroz/PycharmProjects/tese/3DUnetCNN-master/unet3d/generator.py", line 116, in get_validation_split
    nb_samples = data_file.root.data.shape[0]
  File "/home/albaroz/anaconda3/envs/tese/lib/python3.6/site-packages/tables/group.py", line 840, in __getattr__
    return self._f_get_child(name)
  File "/home/albaroz/anaconda3/envs/tese/lib/python3.6/site-packages/tables/group.py", line 712, in _f_get_child
    self._g_check_has_child(childname)
  File "/home/albaroz/anaconda3/envs/tese/lib/python3.6/site-packages/tables/group.py", line 399, in _g_check_has_child
    % (self._v_pathname, name))
tables.exceptions.NoSuchNodeError: group ``/`` does not have a child named ``data``
Closing remaining open files:/home/albaroz/PycharmProjects/tese/3DUnetCNN-master/brats/lits_data.h5...done
Creating validation split...

Process finished with exit code 1

[ellisdg]

tables.exceptions.NoSuchNodeError: group / does not have a child named data

The way I have the code set up, it expects the data file to have 3 groups: “data”, “truth”, and “affine”. You can also add “subject_ids” to the data file as well. During training the generator will fetch the data from the “data” and “truth” groups in the h5 file.

Your problem is that your h5 file does not have the “data” group. It might not have the other groups as well, but missing the “data” group is what caused the error.

Of note, this is the same problem that @SnowRipple had in #95 when trying to create his own h5 file. I got confused when answering his question, and I’m pretty sure I totally messed him up!

[nysuka]

i’m also trying to apply the isensee 3D unet model to the LiTS dataset and was wondering what results @albatroz95 and @love112358 or others are getting with this dataset and architecture. for the liver segmentation, i’m getting mean dice of 0.918 +/- 0.049, median of 0.927, min of 0.693, max of 0.955. even though the scores appear high, some of the edges do not match the manually segmented edges well for the whole liver. the liver tumors did not perform well at all. interested in suggestions to improve.