Predictive Image Registration
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README.md

README.md

quicksilver

This repository contains code and data for the following paper [arXiv]:

@misc{YangKwittStynerNiethammer17a,
    title        = {Quicksilver: Fast Predictive Image Registration - a Deep Learning Approach},
    author       = {X. Yang and R. Kwitt and M. Styner and M. Niethammer},
    year         = {2017},
    howpublished = {arXiv:1703.10908}}

Disclaimer

This software is published for academic and non-commercial use only (Apache-2.0)

Setup

This code is based or PyTorch and PyCA. It has been tested on Ubuntu 14.04/16.04 LTS with Python 2.7 (using Nvidia TitanX GPUs, with CUDA 8.0).

IMPORTANT

The code is currently based on PyTorch 0.3. As some changes to the tensor interface were made in PyTorch 0.4 it currently does not run with PyTorch > 0.3. We will fix this in the near future. For now simply use PyTorch 0.3 or help us port the code :)

Dependencies:

Remark: NiftyReg is used for optional affine pre-alignment to the ICBM152 atlas before performing deformable registration. scikit-image is used for histogram equalization of the input images. Note: if you use Anaconda as the development platform, you can install scikit-image as suggested in the Anaconda page.

Exemplary system configuration

We recommend using Anaconda as your development platform, as this cleanly separates the Python/PyTorch installation (and all required libraries) from your system libraries. We exemplify such an installation below, assuming that the full installation is done under /scratch and CUDA (8.0) is installed under /usr/local/cuda.

Install Anaconda 4.3.1 (Python 2.7)

mkdir /scratch
cd /scratch
wget https://repo.continuum.io/archive/Anaconda2-4.3.1-Linux-x86_64.sh
bash Anaconda2-4.3.1-Linux-x86_64.sh

Follow the installation instructions. We assume that you installed Anaconda under /scratch/anaconda2.

Install PyCA

For our code we use a specific version of PyCA, so please use the following command to download the PyCA code:

cd /scratch
git clone git@bitbucket.org:scicompanat/pyca.git
cd ./pyca
git checkout 9954dd5319efaa0ac5f58977e57acf004ad73ed7
mkdir Build && cd Build
ccmake ...

Configure (according to your system settings) and compile PyCA. Note that we also made a PyCA code clone in quicksilver/3rd_party_software, so you could build PyCA using that.

Final configuration

Finally, we clone the Quicksilver repository as

cd /scratch
git clone https://github.com/rkwitt/quicksilver.git

and create a config file conda.cfg with the following content:

export PATH=$PATH:/usr/local/cuda/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64
export PYTHONPATH=$PYTHONPATH:/scratch/pyca/Build/python_module
export CUDA_HOME=/usr/local/cuda
export PATH="/scratch/anaconda2/bin:$PATH"

Source this file with source conda.cfg to setup the environment.

Usage

Below is a simple quickstart guide on how to use Quicksilver for image-to-image registration (more to come).

Test data

Four (pre-aligned) example images (from CUMC) can be downloaded here.

Quick start

cd /scratch/quicksilver/code/applications
python qs_predict.py --moving-image moving_1.nii moving_2.nii moving_3.nii ...
                     --target-image target_1.nii target_2.nii target_3.nii ...
		             --output-prefix prefix_1 prefix_2 prefix_3 ...

Add the --use-correct option if want to use correction network.

To use multiple GPUs for prediction, add --n-GPU N option, where N indicates the number of GPUs to use. For maximum performance, combine this option with --batch-size K to specify the number of 3D patches as network input, and set K to be a multiple of N.

Example

In this example, we want to register m1.nii (moving) and m2.nii (target) from the provided example data. As the images are already pre-aligned, no additional affine alignment needs to be done.

cd /scratch2/quicksilver
tar xvfz CUMC_examples.tar.gz
cd code/applications
python qs_predict.py \
    --moving-image ../CUMC_examples/m1.nii \
    --target-image ../CUMC_examples/m2.nii \
    --output-prefix /tmp/

This will generate two files: /tmp/I1.mhd, /tmp/I1.raw (i.e., m1.nii aligned to m2.nii in the coordinate system of m2.nii).

Use the probablistic version of the network

Use quicksilver/code/applications/qs_predict_probablistic.py. There are two main differences compared to qs_predict.py. First, there is an additional option --samples that lets you decide the number of times to sample the network (default is 50). The variance of the deformation is samed as 'phiinv_var.mhd'. Second, there are no correction network for the probabilistic network.

Training a new network from start to finish

  1. Do affine alignment and histogram equalization for the training images using quicksilver/code/tools/preprocessing/affine_and_histogram_eq.py. If using the default atlas (the MNI152 atlas as quicksilver/data/atlas/icbm152.nii), Make sure the training images are in the same coordinate system.
  2. Perform registrations on the training data using quicksilver/code/tools/LDDMM_optimization/CAvmMatching.py
  3. Gather the moving images, target images and initial momentum from LDDMM optimization for training the network. This is done by using quicksilver/code/tools/create_pth.py to gather the images and momentums into .pth.tar files. For example:
cd quicksilver/code/tools/
python ./create_pth.py --files moving_image_1 moving_image_2 moving_image_3 --output moving_image_all.pth.tar
python ./create_pth.py --files target_image_1 target_image_2 target_image_3 --output target_image_all.pth.tar
python ./create_pth.py --files momentum_1 momentum_2 momentum_3 --output momentum_all.pth.tar --momentum

You can seperated the images/momentums into several .pth.tar files to make each .pth.tar file size reasonable. For example:

# make training data part 1
python ./create_pth.py --files moving_image_1 moving_image_2 moving_image_3 --output moving_image_dataset_1.pth.tar
python ./create_pth.py --files target_image_1 target_image_2 target_image_3 --output target_image_dataset_1.pth.tar
python ./create_pth.py --files momentum_1 momentum_2 momentum_3 --output momentum_dataset_1.pth.tar --momentum

# make training data part 2
python ./create_pth.py --files moving_image_4 moving_image_5 moving_image_6 --output moving_image_dataset_2.pth.tar
python ./create_pth.py --files target_image_4 target_image_5 target_image_6 --output target_image_dataset_2.pth.tar
python ./create_pth.py --files momentum_4 momentum_5 momentum_6 --output momentum_dataset_2.pth.tar --momentum

Make sure to make the moving images/target images/momentums have the same order in the .pth.tar files.

  1. Train the prediction network using quicksilver/code/tools/qs_train.py. An example will be
cd quicksilver/code/tools
python qs_train.py \
    --moving-image-dataset moving_image_dataset_1.pth.tar moving_image_dataset_2.pth.tar \
    --target-image-dataset target_image_dataset_1.pth.tar target_image_dataset_2.pth.tar \
    --deformation-parameter momentum_dataset_1.pth.tar momentum_dataset_2.pth.tar \
    --deformation-setting-file ./LDDMM_spec.yaml	\
    --output-name ./prediction_network_parameter.pth.tar

Here LDDMM_spec.yaml defines the setting for the LDDMM optimization algorithm. This information is stored in the network parameter file, and is used when using quicksilver to formulate LDDMM shooting.

  1. Create warp-back target image files and momentum difference (between LDDMM optimization and prediction network) files. This is for training the correction network. This operation is done using quicksilver/code/tools/prepare_correction_training_data.py. An example would be (suppose we have the training files as moving_image_1.pth.tar/moving_image_2.pth.tar, target_image_dataset_1.pth.tar/target_image_dataset_2.pth.tar, and momentum_dataset_1.pth.tar/momentum_dataset_2.pth.tar):
cd quicksilver/code/tools
python prepare_correction_training_data.py \
    --moving-image-dataset moving_image_dataset_1.pth.tar moving_image_dataset_2.pth.tar \
    --target-image-dataset target_image_dataset_1.pth.tar target_image_dataset_2.pth.tar \
    --deformation-parameter momentum_dataset_1.pth.tar momentum_dataset_2.pth.tar \
    --network-parameter ./prediction_network_parameter.pth.tar \
    --warped-back-target-output warped_target_dataset_1.pth.tar warped_target_dataset_1.pth.tar \
    --momentum-residual momentum_diff_1.pth.tar momentum_diff_2.pth.tar
  1. Train the correction network. The procedure is the same as step 4, except (as in this example here) change target_image_dataset_x.pth.tar to warped_target_dataset_x.pth.tar and momentum_dataset_1.pth.tar to momentum_diff_1.pth.tar, and of course change the output file name.

evaluate your result on the 4 test datasets

  1. Perform prediction on the four test datasets (CUMC12, LPBA40, MGH10, IBSR18) use qs_predict.py
  2. Calculate the label overlapping score for each test case using calculate_CUMC_overlap.m, calculate_LPBA_overlap.m, calculate_IBSR_overlap.m, calculate_MGH_overlap.m in the quicksilver/code/tools/evaluate_result/ directory
  3. Plot the results and compared to the results in the Neuroimage paper by using quicksilver/code/tools/evaluate_result/generate_label_overlapping_plot.m

An example case to retrain the Quicksilver network:

Below shows an example to train the Quicksilver network using the OASIS dataset. Suppose everything happens in /mydirectory/, and quicksilver is downloaded at /mydirectory/quicksilver/

  1. Download the OASIS dataset from TODO: add OASIS link here. Download the images into /mydirectory/OASIS/
  2. Perform LDDMM registration using the files in /mydirectory/quicksilver/full_quicksilver_walkthrough/step2/. Specifically, run the fullowing bash shell script
cd /mydirectory/quicksilver/code/tools/LDDMM_optimization

for i in $(find /mydirectory/quicksilver/full_quicksilver_walkthrough/step2 -name 'deep_network*.yaml');
do
        python ./CAvmMatching.py $i;
done
  1. Gather all registration resuls into .pth.tar files.
cd /mydirectory/quicksilver/code/tools/
bash /mydirectory/quicksilver/full_quicksilver_walkthrough/step3/gather_data.sh
  1. Train the prediction network:
cd /mydirectory/quicksilver/code/tools/
python ./qs_train.py --moving-image-dataset \
                     /mydirectory/OASIS/OASIS_moving_1.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_2.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_3.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_4.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_5.pth.tar \
                     --target-image-dataset \
                     /mydirectory/OASIS/OASIS_target_1.pth.tar \
                     /mydirectory/OASIS/OASIS_target_2.pth.tar \
                     /mydirectory/OASIS/OASIS_target_3.pth.tar \
                     /mydirectory/OASIS/OASIS_target_4.pth.tar \
                     /mydirectory/OASIS/OASIS_target_5.pth.tar \
                     --deformation-parameter \
                     /mydirectory/OASIS/OASIS_m0_1.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_2.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_3.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_4.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_5.pth.tar \
                     --deformation-setting-file ./LDDMM_spec.yaml \
                     --output-name /mydirectory/prediction_network.pth.tar \
                     --epochs 10
  1. Create the data needed to train the correction network
cd /mydirectory/quicksilver/code/tools/
python prepare_correction_training_data.py --moving-image-dataset \
                     /mydirectory/OASIS/OASIS_moving_1.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_2.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_3.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_4.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_5.pth.tar \
                     --target-image-dataset \
                     /mydirectory/OASIS/OASIS_target_1.pth.tar \
                     /mydirectory/OASIS/OASIS_target_2.pth.tar \
                     /mydirectory/OASIS/OASIS_target_3.pth.tar \
                     /mydirectory/OASIS/OASIS_target_4.pth.tar \
                     /mydirectory/OASIS/OASIS_target_5.pth.tar \
                     --deformation-parameter \
                     /mydirectory/OASIS/OASIS_m0_1.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_2.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_3.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_4.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_5.pth.tar \
                     --network-parameter /mydirectory/prediction_network.pth.tar \
                     --warped-back-target-output \
                     /mydirectory/OASIS/OASIS_target_warpback_1.pth.tar \
                     /mydirectory/OASIS/OASIS_target_warpback_2.pth.tar \
                     /mydirectory/OASIS/OASIS_target_warpback_3.pth.tar \
                     /mydirectory/OASIS/OASIS_target_warpback_4.pth.tar \
                     /mydirectory/OASIS/OASIS_target_warpback_5.pth.tar \
                     --momentum-residual \
                     /mydirectory/OASIS/OASIS_m0_diff_1.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_diff_2.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_diff_3.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_diff_4.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_diff_5.pth.tar
  1. Train the correction network
cd /mydirectory/quicksilver/code/tools/
python ./qs_train.py --moving-image-dataset \
                     /mydirectory/OASIS/OASIS_moving_1.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_2.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_3.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_4.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_5.pth.tar \
                     --target-image-dataset \
                     /mydirectory/OASIS/OASIS_target_warpback_1.pth.tar \
                     /mydirectory/OASIS/OASIS_target_warpback_2.pth.tar \
                     /mydirectory/OASIS/OASIS_target_warpback_3.pth.tar \
                     /mydirectory/OASIS/OASIS_target_warpback_4.pth.tar \
                     /mydirectory/OASIS/OASIS_target_warpback_5.pth.tar \
                     --deformation-parameter \
                     /mydirectory/OASIS/OASIS_m0_diff_1.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_diff_2.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_diff_3.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_diff_4.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_diff_5.pth.tar \
                     --deformation-setting-file ./LDDMM_spec.yaml \
                     --output-name /mydirectory/correction_network.pth.tar \
                     --epochs 10

If you want to train the probablistic version of the network, change the command in step 4 into

cd /mydirectory/quicksilver/code/tools/
python ./qs_train.py --moving-image-dataset \
                     /mydirectory/OASIS/OASIS_moving_1.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_2.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_3.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_4.pth.tar \
                     /mydirectory/OASIS/OASIS_moving_5.pth.tar \
                     --target-image-dataset \
                     /mydirectory/OASIS/OASIS_target_1.pth.tar \
                     /mydirectory/OASIS/OASIS_target_2.pth.tar \
                     /mydirectory/OASIS/OASIS_target_3.pth.tar \
                     /mydirectory/OASIS/OASIS_target_4.pth.tar \
                     /mydirectory/OASIS/OASIS_target_5.pth.tar \
                     --deformation-parameter \
                     /mydirectory/OASIS/OASIS_m0_1.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_2.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_3.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_4.pth.tar \
                     /mydirectory/OASIS/OASIS_m0_5.pth.tar \
                     --deformation-setting-file ./LDDMM_spec.yaml \
                     --output-name /mydirectory/prediction_network.pth.tar \
                     --epochs 10 \ 
                     --use-dropout

and skip step 5 and 6.