MIScnn

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Can you please guide about no of samples in the one epoch for training a network.

4

Hi, Thanks for this wonderful github repo. I am trying to train a model. I have total 200 cases for segmentation. I have following code. data_augmenter = miscnn.Data_Augmentation(cycles=2, scaling=True, rotations=True,...

ramchandracheke

Kits-19.ipynb

5

Hi, When I am executing the crossvalidation function it is showing the following error. Temporary files are created in the batches directory. [Error_file.txt](https://github.com/frankkramer-lab/MIScnn/files/8212905/Error_file.txt)

sreeharih

Normalization and Clipping

1

Hello, Just hoping for some insight as to why pixel values were clipped from -79 to 304 in the KiTS19 example. Does this relate to the window/level operation on images?...

lcaronson

Strategies to Resampling?

1

Let's say, 3D data with shape `(height, width, depth)`. Now, the `depth` is `100`. After doing some eda, we've found that, out of 100 slices, most of them are black,...

innat

Which standard configuration to use when comparing MISccn to other methods?

2

Hi I have MIScnn shortlisted as a candidate to be included on our work to find the best openly available method to autosegment head and neck cancer (HNC) tumors on...

davidkvcs

Clarification?

9

I've some queries regarding the approach in the code. 1. [HERE](https://github.com/frankkramer-lab/covid19.MIScnn/blob/master/scripts/run_miscnn.py#L84-L88), you set `analysis="patchwise-crop", patch_shape=(160, 160, 80)`. What does this `analysis` param exactly mean? And what is the relation with...

innat

Have a look in batchgenerators MirrorTransform with newest version 0.23. Image Augmentation unittesting throwing errors that no augmentation is done when it should mirror volumes. Investigation in a separate google...

muellerdo

https://github.com/keras-team/keras/issues/3653 https://github.com/keras-team/keras/issues/3653#issuecomment-761085597 https://tensorflow.google.cn/tutorials/images/segmentation?hl=en&skip_cache=true%22 - Implement class dictionary as parameter for data generator - if parameter != None, compute sample weight according to GitHubUser97 answer (with dynamic n_classes) - Return sample...

muellerdo

Quick question re: final Dice coefficient values

1

Hello Dominik, In your paper in BMC you mention kidney Dice coefficients and tumor Dice coefficients. How did you get the algorithm to output a separate Dice coefficient for kidneys...

lcaronson

Input 0 of layer "batch_normalization" is incompatible with the layer: expected ndim=4, found ndim=5. Full shape received: (None, None, None, None, 32)

3

Can you please let me know, what I am getting this error? How to fix it? Thanks, Sidra

aleemsidra