06 Apr

A temporally consistent atlas of neonatal brain development

Excited to present my work on temporally consistent modelling of the neonatal brain morphology from structural brain magnetic resonance (MR) images at the Centre for the Developing Brain at King’s College London, St’ Thomas Hospital.

Axial mid-sections of mean intensity and shape templates at 40 weeks PMA.

After providing some background on brain atlas construction, the talk focuses on our novel group-wise approach for the construction of an unbiased spatio-temporal brain with improved temporal consistency, lower computational cost, and considerably higher cortical detail than previous neonatal atlas construction techniques. It is a summary of our work detailed in Schuh et al., “Unbiased construction of a temporally consistent morphological atlas of neonatal brain development”, preprint available on bioRxiv (doi:10.1101/251512).

13 May

dHCP: News coverage of first data release

3D reconstruction of the cortical surface and calculated features from a seven-month, eight-month and nine-month baby brain MRI.

The first batch of data acquired and processed as part of the Developing Human Connectome Project has been released, with articles about the project published by BBC and The Guardian. These feature colourful renders of cortical surfaces reconstructed from MRI scans of neonatal brains using our approach presented at ISBI 2017.

11 Apr

dHCP: Neonatal Cortex Reconstruction

A preprint of our article “The Developing Human Connectome Project: a Minimal Processing Pipeline for Neonatal Cortical Surface Reconstruction”, covering the full structural image processing steps, following the MR volume reconstruction, from whole brain segmentation to the reconstruction and spherical mapping of the neonatal cortex, is now available on bioRxiv (doi:10.1101/125526).

10 Jan

Paper accepted at ISBI 2017

Our paper on deformable models for the reconstruction of the neonatal cortex from structural T2-weighted brain MR images was accepted for presentation at the 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI) which takes place this year April 18-21 in Melbourne, Australia.

A deformable model for the reconstruction of the neonatal cortex

Two stages of deformable mesh reconstruction of one hemisphere of a white matter surface. Colour depicts residual distance.

We present a method based on deformable meshes for the reconstruction of the cortical surfaces of the developing human brain at the neonatal period. It employs a brain segmentation for the reconstruction of an initial inner cortical surface mesh. Errors in the segmentation resulting from poor tissue contrast in neonatal MRI and partial volume effects are subsequently accounted for by a local edge-based refinement. We show that the obtained surface models define the cortical boundaries more accurately than the segmentation. The surface meshes are further guaranteed to not intersect and subdivide the brain volume into disjoint regions. The proposed method generates topologically correct surfaces which facilitate both a flattening and spherical mapping of the cortex.

22 Apr

MIRTK Release 1.1

I have just released MIRTK version 1.1.

This release gets rid of bugs, runs on Linux, OS X, and Windows, and provides a Python package for execution of MIRTK commands in a pipeline script. The commands now support the NIfTI-2 image file format for large images and the GIFTI file format for cortical surface meshes as used by the HCP project. The build system has further improved with CMake BASIS 3.3 and automated builds help to keep the project stable.

An Ubuntu 14.04 Docker image with MIRTK pre-installed is available from Docker Hub the quickest way to getting to know MIRTK or to perform reproducible experiments in a confined environment!

See Release Notes for a complete list of changes.

22 Apr

BASIS Release 3.3

This release starts a new era in the development of the CMake BASIS project. Many artifacts from its origins have been discarded from the revision history to move forward with a lighter and easier to integrate repository. This version of CMake BASIS includes a number of fixes and improvements, mainly driven by the project modularization and CMake BASIS Modules integration demands of the MIRTK project.

See Release Notes for more information.

10 Sep


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