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

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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