A new fast accurate nonlinear medical image registration program including surface preserving regularization

Unsupervised machine learning identifies predictive progression markers of IPF

OBJECTIVES

To identify and evaluate predictive lung imaging markers and their pathways of change during progression of idiopathic pulmonary fibrosis (IPF) from sequential data of an IPF cohort. To test if these imaging markers predict outcome.

METHODS

We studied radiological disease progression in 76 patients with IPF, including overall 190 computed tomography (CT) examinations of the chest. An algorithm identified candidates for imaging patterns marking progression by computationally clustering visual CT features. A classification algorithm selected clusters associated with radiological disease progression by testing their value for recognizing the temporal sequence of examinations. This resulted in radiological disease progression signatures, and pathways of lung tissue change accompanying progression observed across the cohort. Finally, we tested if the dynamics of marker patterns predict outcome, and performed an external validation study on a cohort from a different center.

RESULTS

Progression marker patterns were identified and exhibited high stability in a repeatability experiment with 20 random sub-cohorts of the overall cohort. The 4 top-ranked progression markers were consistently selected as most informative for progression across all random sub-cohorts. After spatial image registration, local tracking of lung pattern transitions revealed a network of tissue transition pathways from healthy to a sequence of disease tissues. The progression markers were predictive for outcome, and the model achieved comparable results on a replication cohort.

CONCLUSIONS

Unsupervised learning can identify radiological disease progression markers that predict outcome. Local tracking of pattern transitions reveals pathways of radiological disease progression from healthy lung tissue through a sequence of diseased tissue types.

KEY POINTS

• Unsupervised learning can identify radiological disease progression markers that predict outcome in patients with idiopathic pulmonary fibrosis. • Local tracking of pattern transitions reveals pathways of radiological disease progression from healthy lung tissue through a sequence of diseased tissue types. • The progression markers achieved comparable results on a replication cohort.

Performance-aware programming for intraoperative intensity-based image registration on graphics processing units

Purpose

Intensity-based image registration has been proven essential in many applications accredited to its unparalleled ability to resolve image misalignments. However, long registration time for image realignment prohibits its use in intra-operative navigation systems. There has been much work on accelerating the registration process by improving the algorithm’s robustness, but the innate computation required by the registration algorithm has been unresolved.

Methods

Intensity-based registration methods involve operations with high arithmetic load and memory access demand, which supposes to be reduced by graphics processing units (GPUs). Although GPUs are widespread and affordable, there is a lack of open-source GPU implementations optimized for non-rigid image registration. This paper demonstrates performance-aware programming techniques, which involves systematic exploitation of GPU features, by implementing the diffeomorphic log-demons algorithm.

Results

By resolving the pinpointed computation bottlenecks on GPU, our implementation of diffeomorphic log-demons on Nvidia GTX Titan X GPU has achieved ~ 95 times speed-up compared to the CPU and registered a 1.3-M voxel image in 286 ms. Even for large 37-M voxel images, our implementation is able to register in 8.56 s, which attained ~ 258 times speed-up. Our solution involves effective employment of GPU computation units, memory, and data bandwidth to resolve computation bottlenecks.

Conclusion

The computation bottlenecks in diffeomorphic log-demons are pinpointed, analyzed, and resolved using various GPU performance-aware programming techniques. The proposed fast computation on basic image operations not only enhances the computation of diffeomorphic log-demons, but is also potentially extended to speed up many other intensity-based approaches. Our implementation is open-source on GitHub at https://bit.ly/2PYZxQz.

Variability of computed tomography radiomics features of fibrosing interstitial lung disease: A test-retest study

OBJECTIVES

To investigate the intra- and inter-scanner repeatability and reproducibility of CT radiomics features (RF) of fibrosing interstitial lung disease (fILD).

METHODS

For this prospective, IRB-approved test-retest study, CT data of sixty fILD patients were acquired. Group A (n = 30) underwent one repeated CT scan on a single scanner. Group B (n = 30) was scanned using two different CT scanners. All CT data were reconstructed using different reconstruction kernels (soft, intermediate, sharp) and slice thicknesses (one and three millimeters), resulting in twelve datasets per patient. Following ROI placement in fibrotic lung tissue, 86 RF were extracted. Intra- and inter-scanner RF repeatability and reproducibility were assessed by calculating intraclass correlation coefficients (ICCs) for corresponding kernels and slice thicknesses, and between lung-specific and non-lung-specific reconstruction parameters. Furthermore, test-retest lung volumes were compared.

RESULTS

Test-retest demonstrated a majority of RF is highly repeatable for all reconstruction parameter combinations. Intra-scanner reproducibility was negatively affected by reconstruction kernel changes, and further reduced by slice thickness alterations. Inter-scanner reproducibility was highly variable, reconstruction parameter-specific, and greatest if either soft kernels and three-millimeter slice thickness, or lung-specific reconstruction parameters were used for both scans. Test-retest lung volumes showed no significant difference.

CONCLUSION

CT RF of fILD are highly repeatable for constant reconstruction parameters in a single scanner. Intra- and inter-scanner reproducibility are severely impacted by alterations in slice thickness more than reconstruction kernel, and are reconstruction parameter-specific. These findings may facilitate CT data and RF selection and assessment in future fILD radiomics studies collecting data across scanners.

Symplectomorphic registration with phase space regularization by entropy spectrum pathways

PURPOSE

The ability to register image data to a common coordinate system is a critical feature of virtually all imaging studies. However, in spite of the abundance of literature on the subject and the existence of several variants of registration algorithms, their practical utility remains problematic, as commonly acknowledged even by developers of these methods.

METHODS

A new registration method is presented that utilizes a Hamiltonian formalism and constructs registration as a sequence of symplectomorphic maps in conjunction with a novel phase space regularization. For validation of the framework a panel of deformations expressed in analytical form is developed that includes deformations based on known physical processes in MRI and reproduces various distortions and artifacts typically present in images collected using these different MRI modalities.

RESULTS

The method is demonstrated on the three different magnetic resonance imaging (MRI) modalities by mapping between high resolution anatomical (HRA) volumes, medium resolution diffusion weighted MRI (DW-MRI) and HRA volumes, and low resolution functional MRI (fMRI) and HRA volumes.

CONCLUSIONS

The method has shown an excellent performance and the panel of deformations was instrumental to quantify its repeatability and reproducibility in comparison to several available alternative approaches.

Three-Dimensional Digital Template Atlas of the Macaque Brain

We present a new 3D template atlas of the anatomical subdivisions of the macaque brain, which is based on and aligned to the magnetic resonance imaging (MRI) data set and histological sections of the Saleem and Logothetis atlas. We describe the creation and validation of the atlas that, when registered with macaque structural or functional MRI scans, provides a straightforward means to estimate the boundaries between architectonic areas, either in a 3D volume with different planes of sections, or on an inflated brain surface (cortical flat map). As such, this new template atlas is intended for use as a reference standard for macaque brain research. Atlases and templates are available as both volumes and surfaces in standard NIFTI and GIFTI formats.