Unpaired prostate ultrasound registration¶
Note: Please read the DeepReg Demo Disclaimer.
This DeepReg Demo is also an example of cross validation.
Author¶
DeepReg Development Team
Application¶
Transrectal ultrasound (TRUS) images are acquired from prostate cancer patients during image-guided procedures. Pairwise registration between these 3D images may be useful for intraoperative motion modelling and group-wise registration for population studies.
Data¶
The 3D ultrasound images used in this demo were derived from the Prostate-MRI-US-Biopsy dataset, hosted at the Cancer Imaging Archive (TCIA).
Instruction¶
Change current directory to the root directory of DeepReg project;
Run
demo_data.py
script to download 10 folds of unpaired 3D ultrasound images;
python demos/unpaired_us_prostate_cv/demo_data.py
Call
deepreg_train
from command line. The following example uses three GPUs and launches the first of the ten runs of a 9-fold cross-validation, as specified in the ``dataset` section <./unpaired_us_prostate_cv_run1.yaml>`_ and the ``train` section <./unpaired_us_prostate_cv_train.yaml>`_, which can be specified in separate yaml files. The 10th fold is reserved for testing;
deepreg_train --gpu "1, 2, 3" --config_path demos/unpaired_us_prostate_cv/unpaired_us_prostate_cv_run1.yaml demos/unpaired_us_prostate_cv/unpaired_us_prostate_cv_train.yaml --log_dir unpaired_us_prostate_cv
Call
deepreg_predict
from command line to use the saved ckpt file for testing on the 10th fold data. The following example uses a pre-trained model, on CPU. If not specified, the results will be saved at the created timestamp-named directories under /logs.
deepreg_predict --gpu "" --config_path demos/unpaired_us_prostate_cv/unpaired_us_prostate_cv_run1.yaml demos/unpaired_us_prostate_cv/unpaired_us_prostate_cv_train.yaml --ckpt_path demos/unpaired_us_prostate_cv/dataset/pre-trained/weights-epoch5000.ckpt --mode test
Pre-trained Model¶
A pre-trained model will be downloaded after running demo_data.py
and unzipped at the
dataset folder under the demo folder. This pre-trained model will be used by default
with deepreg_predict
. Run the user-trained model by specifying with --ckpt_path
the
location where the ckpt files will be saved, in this case (specified by deepreg_train
as above), /logs/unpaired_us_prostate_cv/.
Tested DeepReg version¶
Last commit at which demo was tested: 7bec018b5e910f1589888f3f286e9f6a11060c31
Contact¶
Please raise an issue.