A research-focused toolkit developed within the GIFT-Surg project to reconstruct a volumetric representation from printed brain MR films.
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README.md

Volumetric Reconstruction from Printed Films

This is a Python-based open-source toolkit for research developed within the GIFT-Surg project to reconstruct a volumetric representation from printed brain MR films as described in Ebner et al., 2018.

The algorithm and software were developed by Michael Ebner at the Translational Imaging Group in the Centre for Medical Image Computing at University College London (UCL). Please note that currently only Python 2 is supported.

If you have any questions or comments, please drop an email to michael.ebner.14@ucl.ac.uk.

How it works

  1. Run the Semi-Automatic Slice Extraction Tool: A semi-automatic slice extraction tool is used to create a digital image stack from printed slices selected from the scanned brain MR films. It provides an initial digital 3D representation of acquired slices printed on a 2D film where the correct spatial position and dimension of each single slice needs to be recovered.

  2. Recover Meta-Data Information and Correct for In-plane Motion: A fully automatic volumetric reconstruction framework to estimate the lost meta-data information of each slice in the 3D space. It is based on a joint slice-to-volume affine registration with inter-slice 2D transformation regularisation and affine slice-intensity correction. Missing meta-data information is contributed by a longitudinal scan of the same subject.

  3. Recover the 3D Volume using Isotropic Total Variation Denoising: A final isotropic total variation in-plane deconvolution technique serves to revitalise the visual appearance of the reconstructed stack of printed slices.

How to cite

If you use this software in your work, please cite Ebner et al., 2018.

  • Ebner, M., Chung, K. K., Prados, F., Cardoso, M. J., Chard, D. T., Vercauteren, T., & Ourselin, S. (2018). Volumetric reconstruction from printed films: Enabling 30 year longitudinal analysis in MR neuroimaging. NeuroImage, 165, 238–250.

Installation

This toolkit is currently supported for Python 2 only and was tested on

  • Mac OS X 10.10 and 10.12
  • Ubuntu 14.04 and 16.04

It builds on a couple of additional libraries developed within the GIFT-Surg project including

whose installation requirements need to be met:

  1. Installation of ITK_NiftyMIC
  2. Installation of SimpleReg dependencies

Afterwards, clone this repository via

  • git clone git@github.com:gift-surg/VolumetricReconstructionFromPrintedFilms.git

where all remaining dependencies can be installed using pip:

  • pip install -r requirements.txt
  • pip install -e .

Note, that we suggest using the matplotlib version 1.4.3 as more recent versions (we tried matplotlib >= 2.0.0) may slow down the visualization performance of the semi-automatic slice extraction tool substantially.

Check installation via

  • python -m nose tests/installation_test.py

Example usage

Run the semi-automatic slice extraction tool to create a a digital image stack from printed slices:

vrpf_extract_stack_from_films \
--films path-to-film1.dcm ... path-to-filmN.dcm \
--stack path-to-extracted-stack.nii.gz \
--inplane-spacing initial-guess-in-plane-spacing \
--slice-thickness known-slice-thickness

The current version accepts DICOM (.dcm) and NIfTI (.nii or .nii.gz) as input film types. A handbook on how to use the semi-automatic slice extraction tool can be found in doc/.


Recover the meta-data information and correct for in-plane motion of each individual slice by using a reference volume.

vrpf_correct_motion \
--stack path-to-extracted-stack.nii.gz \
--reference path-to-reference-volume.nii.gz \
--dir-output output-directory-for-motion-correction-results \
--dir-output-verbose output-directory-for-intermediate-results

Estimated transform parameters for both in-plane similarity and affine transforms are written to the output directory for each single slice in separate folders called Similarity and Affine, respectively. It is possible to run in-plane rigid motion correction only by setting the flag --rigid-only 1 which will write the obtained motion correction results to the folder Rigid instead. The obtained motion correction results are used as input for vrpf_reconstruct_volume.py which provides a volumetric reconstruction in a subsequent step.


Based on the estimated transformations a volumetric representation is reconstructed. An additional total variation denoising step is performed for improved visual appearance.

An example call reads:

vrpf_reconstruct_volume \
--stack path-to-extracted-stack.nii.gz \
--reference path-to-reference-volume.nii.gz \
--dir-input path-to-motion-correction-results/Similarity \
--dir-output output-directory \
--regularization TV \
--alpha 0.005 \
--sigma2 0.25

In case a negative variance is provided, e.g. --sigma2 -1, the in-plane deblurring is estimated automatically from the pixel dimensions of stack.

Licensing and Copyright

Copyright (c) 2017, University College London. This framework is made available as free open-source software under the BSD-3-Clause License. Other licenses may apply for dependencies.

Funding

This work is partially funded by the UCL Engineering and Physical Sciences Research Council (EPSRC) Centre for Doctoral Training in Medical Imaging (EP/L016478/1), the Innovative Engineering for Health award (Wellcome Trust [WT101957] and EPSRC [NS/A000027/1]), the Multiple Sclerosis Society of Great Britain and Northern Ireland (grant references 20 and 984) and supported by researchers at the National Institute for Health Research University College London Hospitals (UCLH) Biomedical Research Centre. FP is supported by the Guarantors of Brain.