mednist_reg

MedNIST Hand Image Registration

Based on the tutorial of 2D registration

Downloading the Dataset

Download the dataset from here and extract the contents to a convenient location.

The MedNIST dataset was gathered from several sets from TCIA, the RSNA Bone Age Challenge, and the NIH Chest X-ray dataset.

The dataset is kindly made available by Dr. Bradley J. Erickson M.D., Ph.D. (Department of Radiology, Mayo Clinic) under the Creative Commons CC BY-SA 4.0 license.

If you use the MedNIST dataset, please acknowledge the source.

Training

Training with same-subject image inputs

python -m monai.bundle run training --config_file configs/train.yaml --dataset_dir "/workspace/data/MedNIST/Hand"

Training with cross-subject image inputs

python -m monai.bundle run training \
  --config_file configs/train.yaml \
  --dataset_dir "/workspace/data/MedNIST/Hand" \
  --cross_subjects True

Training from an existing checkpoint file, for example, models/model_key_metric=-0.0734.pt:

python -m monai.bundle run training --config_file configs/train.yaml [...omitting other args] --ckpt "models/model_key_metric=-0.0734.pt"

Inference

The following figure shows an intra-subject (--cross_subjects False) model inference results (Fixed, moving and predicted images from left to right)

The command shows an inference workflow with the checkpoint "models/model_key_metric=-0.0890.pt" and using device "cuda:1":

python -m monai.bundle run eval \
  --config_file configs/inference.yaml \
  --ckpt "models/model_key_metric=-0.0890.pt" \
  --logging_file configs/logging.conf \
  --device "cuda:1"

Fine-tuning for cross-subject alignments

The following commands starts a finetuning workflow based on the checkpoint "models/model_key_metric=-0.0065.pt" for 5 epochs using the global mutual information loss.

python -m monai.bundle run training \
  --config_file configs/train.yaml \
  --cross_subjects True \
  --ckpt "models/model_key_metric=-0.0065.pt" \
  --lr 0.000001 \
  --trainer#loss_function "@mutual_info_loss" \
  --max_epochs 5

The following figure shows an inter-subject (--cross_subjects True) model inference results (Fixed, moving and predicted images from left to right)

Visualize the first pair of images for debugging (requires matplotlib)

python -m monai.bundle run display --config_file configs/train.yaml

python -m monai.bundle run display --config_file configs/train.yaml --cross_subjects True

License

Copyright (c) MONAI Consortium

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.