input.yaml

# KiTS23 Auto3DSeg user input

modality: CT                        # primary modality
dataroot: /data/kits23              # dataset location
datalist: kits23_folds.json         # a list of filenames
class_names:                        # names for tensorboard, and label index grouping specific for KiTS data
  - { name: kidney_and_mass, index: [1,2,3] }
  - { name: mass, index: [2,3] }
  - { name: tumor, index: [2] }

# OPTIONAL
# use final sigmoid activation (instead of the default softmax), since KiTS regions are overlapping (multi-label segmentation)
# this is optional to set, the system auto-detects overlapping labels automatically.
sigmoid: true

# the config below is optional, but it explicitly sets params as it was used during KiTS23 challenge
# otherwise, the defaults are used, auto_scale_allowed is True and the system will attempt to guess these settings according to the available GPU (e.g. make batch size larger)
auto_scale_allowed: false
num_epochs: 600
resample: true
resample_resolution: [0.78125, 0.78125, 0.78125]
roi_size: [256, 256, 256]
# roi_size: [336, 336, 336]
# loss: {_target_: DiceLoss}
# batch_size: 1
# augment_mode: ct_ax_1