***Unofficial*** Guide to the HCP surface file formats

The WU-Minn Human Connectome Project has provided an immensely powerful resource of 1000 adult subjects functional and structural imaging data, all projected to the surface. This resource has already begun to generate high impact publications and huge leap forwards in understand macroscale brain structure and its influences on human behaviour [1][2]. Nevertheless the data sets… Continue reading ***Unofficial*** Guide to the HCP surface file formats

Multimodal Surface Matching (MSM): a flexible tool for aligning generic data on the cortical surface

Let’s say you have run a functional imaging experiment on a group of different subjects: you have asked all the subjects to perform a task in the scanner, and you want to know whether the response of all subjects to that task is the same. For example, you have some healthy subjects, and some with… Continue reading Multimodal Surface Matching (MSM): a flexible tool for aligning generic data on the cortical surface

Tricks to Implementing QPBO and the ELC: MRF optimisation library

It seems that many people are having trouble compiling Kolmogorov’s QPBO MRF optimisation library for Mac OS, and clang. So, I thought I’d post some tips on how I did it, albeit with considerable help from those more knowledgeable in good c++ practice than myself! There seems to be a problem with the implementation of… Continue reading Tricks to Implementing QPBO and the ELC: MRF optimisation library

The future of connectome modelling lies in multi-modal imaging

Simple models of functional or structural connectivity are insufficient to fully characterise the macroscale connectome. This was the overriding message conveyed from a series of talks organised at Imperial this week, starting with two excellent methods talks from FMRIB Oxford, and culminating in an inspiring overview of connectome research: past, present and future from Professor… Continue reading The future of connectome modelling lies in multi-modal imaging

Autism spectrum disorder: An Ethical dilemma facing connectomics research?

Our understanding of Autism, and its variants, has grown rapidly since it was first discussed by Hans Asperger and Leo Kanner in the 1930s and 40s. Yet, although only half of those diagnosed with the condition experience intellectual disability, there is still stigma attached to the condition. In a new book (NeuroTribes: The Legacy of Autism and the… Continue reading Autism spectrum disorder: An Ethical dilemma facing connectomics research?

Science communication masterclass

Screenhouse, a science broadcasting company run a media communication workshop in association with Dr Maggie Aderin-Pocock, the “Sky at Night” Presenter. They propose techniques for presenting science to the public in a clearer and more exciting way, using: catchy headlines, shorter sentences, soundbites and analogies. Two pieces of advice particularly struck me: the first was to think like… Continue reading Science communication masterclass

Imperial Festival: Baby’s first home video presentation

As part of the Imperial festival, myself and colleagues presented some our of work relating to fetal MRI. MRI imaging is a non invasive imaging technique that uses the water content of tissues as contrast. This makes it a very safe imaging modality with exceptional resolution, and wide flexibility to also image, blood flow, brain… Continue reading Imperial Festival: Baby’s first home video presentation

Multimodal data fusion on the cortex: neuroscientific basis and challenges facing joint inference

A few months ago, my colleagues suggested that I attempt to give a neuroscience overview to the rest of our group. As computer scientists and image processing specialists working in the medical imaging arena, we know surprisingly little about neuro-anatomy or the origins of the signals we are are  processing. As neuroscience methods developers we… Continue reading Multimodal data fusion on the cortex: neuroscientific basis and challenges facing joint inference