OHBM ON-DEMAND HOW-TO: REPRODUCIBILITY AND GOOD NEUROIMAGING PRACTICES
Written by: Claude Bajada, Fakhereh Movahedian Attar, Ilona Lipp
Expert reviewers: Adina Wagner, Cyril Pernet
Newbie editors: Yana Dimech, Renzo Torrecuso
Introduction
This post is about good neuroimaging practices. ‘Practices’ relates to all aspects of conducting research. By ‘good’, we mean beneficial to the field and neuroimaging community - but you’ll see that most of these practices also benefit the individual researcher. Here, we collected a number of tools, tips and tricks to do neuroimaging in the ‘best’ way possible. We aim to provide an overview and answer some questions you may have asked yourself about reproducibility and good neuroimaging practices. As usual, we refer to OHBM On-Demand videos from the educational sessions of previous annual meetings.
See full content here: https://www.ohbmbrainmappingblog.com/blog/ohbm-on-demand-how-to-reproducibility-and-good-neuroimaging-practices
ON-DEMAND HOW-TO: MEASURING GABA IN THE BRAIN WITH MR SPECTROSCOPY
Authors: Katie Williams, Ilona Lipp, Mark Mikkelsen
Infographic: Roselyne Chauvin
Expert editors: James Kolasinski, Paul Mullins
Newbie editors: Curtiss Chapman, Yana Dimech
Introduction
The noninvasive imaging tools that we Human Brain Mappers apply are most often being used to research brain structure and function. Neurotransmitter systems are something that we are aware of and use to take into account when coming up with hypotheses or interpreting our findings, but rarely make the direct subject of our investigation. Most of us have probably heard of GABA (gamma-aminobutyric acid) as the principal inhibitory neurotransmitter that is used by many interneurons. That we can also measure GABA in vivo with MR spectroscopy (MRS) is maybe less widely known. While this biomedical imaging tool opens many doors for neuroscience, measurement of GABA using MRS is not broadly used yet, possibly because special sequences and analysis methods are needed. At the OHBM Annual Meeting in 2019, for the first time, an educational session on GABA MRS was held. This post summarizes what was taught about the most important things you need to know if you’re considering GABA MRS for your research.
See full content here: https://www.ohbmbrainmappingblog.com/blog/on-demand-how-to-measuring-gaba-in-the-brain-with-mr-spectroscopy
OHBM ONDEMAND HOW-TO: ANATOMY IN NEUROIMAGING
Authors: Claude Bajada, Nils Muhlert, Ilona Lipp
Infographic: Roselyne Chauvin
Expert editors: Alfred Anwander, Jurgen Gatt
Newbie editor: Caroline Jantzen
Introduction
Neuroanatomy is one of the most exciting topics in neuroscience! Some readers may disagree, but for now, humor us and read along. With the help of this On-Demand post, we will convince you not only that anatomy is a useful endeavour but that it is one where much beauty is found. Our journey starts with the fundamental notion that the structure and the function of objects are tightly coupled; sometimes in ways that are not obvious. Understanding the complexity of the brain’s structure, hopefully, allows researchers to build more accurate models of brain function.
See full content here: https://www.ohbmbrainmappingblog.com/blog/on-demand-how-to-anatomy-in-neuroimaging
OHBM ONDEMAND HOW-TO: DIFFUSION MRI
By Claude Bajada & Ilona Lipp
Introduction
For the budding cerebronaut, the term diffusion MRI evokes images of fancy red, green or blue fibre coursing across the brain; pretty enough to find their way onto a musical album cover or to be the standard stock image for anyone giving a public communication lecture about the brain. While the pictures are appealing, the terminology associated with diffusion MRI is often confusing and hard to disentangle. Any PhD student about to embark on a diffusion MRI project has had to grapple with a sea of acronyms such as DTI, HARDI, FA, RD, ADC, CHARMED and many more! If you have ever got frustrated by these terms and how they relate, this “how-to” post is for you.
See full content here: https://www.ohbmbrainmappingblog.com/blog/ohbm-ondemand-how-to-diffusion-mri
OHBM ONDEMAND HOW-TO: RESTING STATE FMRI ANALYSIS
By Danka Jandric, Jeanette Mumford & Ilona Lipp
Introduction
Planning a resting state study and analysing resting state data can feel overwhelming. There seems to be an endless number of options regarding all stages of the experiment. Decisions need to be made about how to acquire data in an optimal way, what preprocessing and noise correction pipelines to employ and how to extract the most meaningful metrics. Many strategies have been published and are available in software packages. However, there seems to be little consensus about what works best and even more importantly, about how to judge whether something “works” or not. The choice of method often depends on the specifics of the data and addressed research question, but can equally often seem arbitrary. To help guide you through this jungle of rs-fMRI, we walk you through all stages of a resting state experiment. We do this by addressing questions that researchers are likely to have… or should have! While we do not provide definite answers to these questions, we try to point out the most important considerations, outline some of the available methods, and offer some valuable video resources from recent OHBM education courses, to help you make informed decisions.
See full content here: https://www.ohbmbrainmappingblog.com/blog/ohbm-ondemand-how-to-resting-state-fmri-analysis
OHBM ONDEMAND HOW-TO: MACHINE LEARNING IN NEUROIMAGING
By Claude Bajada, Simon M. Hofmann and Ilona Lipp
Edited by: Thomas Yeo and Lisa Nickerson
Introduction
Machine learning, deep learning and artificial intelligence are terms that currently appear everywhere; in the media, in job adverts… and at neuroimaging conferences. Machine learning is often portrayed as a mystical black box that will either solve all our problems in the future or replace us in our jobs. In this blog post, we discuss what the term machine learning actually means, what methods it encompasses, and how these methods can be applied to brain imaging analysis. Doing this, we refer to the OHBM OnDemand material, which contains some great videos explaining machine learning methodology and we provide examples for how it has been used in a variety of applications. If you are curious about machine learning tools, but are not really sure whether you want to jump on the bandwagon, then we hope that this post is right for you and will help you get started.
See full content here: https://www.ohbmbrainmappingblog.com/blog/ohbm-ondemand-how-to-machine-learning-in-neuroimaging
Written by: Claude Bajada, Fakhereh Movahedian Attar, Ilona Lipp
Expert reviewers: Adina Wagner, Cyril Pernet
Newbie editors: Yana Dimech, Renzo Torrecuso
Introduction
This post is about good neuroimaging practices. ‘Practices’ relates to all aspects of conducting research. By ‘good’, we mean beneficial to the field and neuroimaging community - but you’ll see that most of these practices also benefit the individual researcher. Here, we collected a number of tools, tips and tricks to do neuroimaging in the ‘best’ way possible. We aim to provide an overview and answer some questions you may have asked yourself about reproducibility and good neuroimaging practices. As usual, we refer to OHBM On-Demand videos from the educational sessions of previous annual meetings.
See full content here: https://www.ohbmbrainmappingblog.com/blog/ohbm-on-demand-how-to-reproducibility-and-good-neuroimaging-practices
ON-DEMAND HOW-TO: MEASURING GABA IN THE BRAIN WITH MR SPECTROSCOPY
Authors: Katie Williams, Ilona Lipp, Mark Mikkelsen
Infographic: Roselyne Chauvin
Expert editors: James Kolasinski, Paul Mullins
Newbie editors: Curtiss Chapman, Yana Dimech
Introduction
The noninvasive imaging tools that we Human Brain Mappers apply are most often being used to research brain structure and function. Neurotransmitter systems are something that we are aware of and use to take into account when coming up with hypotheses or interpreting our findings, but rarely make the direct subject of our investigation. Most of us have probably heard of GABA (gamma-aminobutyric acid) as the principal inhibitory neurotransmitter that is used by many interneurons. That we can also measure GABA in vivo with MR spectroscopy (MRS) is maybe less widely known. While this biomedical imaging tool opens many doors for neuroscience, measurement of GABA using MRS is not broadly used yet, possibly because special sequences and analysis methods are needed. At the OHBM Annual Meeting in 2019, for the first time, an educational session on GABA MRS was held. This post summarizes what was taught about the most important things you need to know if you’re considering GABA MRS for your research.
See full content here: https://www.ohbmbrainmappingblog.com/blog/on-demand-how-to-measuring-gaba-in-the-brain-with-mr-spectroscopy
OHBM ONDEMAND HOW-TO: ANATOMY IN NEUROIMAGING
Authors: Claude Bajada, Nils Muhlert, Ilona Lipp
Infographic: Roselyne Chauvin
Expert editors: Alfred Anwander, Jurgen Gatt
Newbie editor: Caroline Jantzen
Introduction
Neuroanatomy is one of the most exciting topics in neuroscience! Some readers may disagree, but for now, humor us and read along. With the help of this On-Demand post, we will convince you not only that anatomy is a useful endeavour but that it is one where much beauty is found. Our journey starts with the fundamental notion that the structure and the function of objects are tightly coupled; sometimes in ways that are not obvious. Understanding the complexity of the brain’s structure, hopefully, allows researchers to build more accurate models of brain function.
See full content here: https://www.ohbmbrainmappingblog.com/blog/on-demand-how-to-anatomy-in-neuroimaging
OHBM ONDEMAND HOW-TO: DIFFUSION MRI
By Claude Bajada & Ilona Lipp
Introduction
For the budding cerebronaut, the term diffusion MRI evokes images of fancy red, green or blue fibre coursing across the brain; pretty enough to find their way onto a musical album cover or to be the standard stock image for anyone giving a public communication lecture about the brain. While the pictures are appealing, the terminology associated with diffusion MRI is often confusing and hard to disentangle. Any PhD student about to embark on a diffusion MRI project has had to grapple with a sea of acronyms such as DTI, HARDI, FA, RD, ADC, CHARMED and many more! If you have ever got frustrated by these terms and how they relate, this “how-to” post is for you.
See full content here: https://www.ohbmbrainmappingblog.com/blog/ohbm-ondemand-how-to-diffusion-mri
OHBM ONDEMAND HOW-TO: RESTING STATE FMRI ANALYSIS
By Danka Jandric, Jeanette Mumford & Ilona Lipp
Introduction
Planning a resting state study and analysing resting state data can feel overwhelming. There seems to be an endless number of options regarding all stages of the experiment. Decisions need to be made about how to acquire data in an optimal way, what preprocessing and noise correction pipelines to employ and how to extract the most meaningful metrics. Many strategies have been published and are available in software packages. However, there seems to be little consensus about what works best and even more importantly, about how to judge whether something “works” or not. The choice of method often depends on the specifics of the data and addressed research question, but can equally often seem arbitrary. To help guide you through this jungle of rs-fMRI, we walk you through all stages of a resting state experiment. We do this by addressing questions that researchers are likely to have… or should have! While we do not provide definite answers to these questions, we try to point out the most important considerations, outline some of the available methods, and offer some valuable video resources from recent OHBM education courses, to help you make informed decisions.
See full content here: https://www.ohbmbrainmappingblog.com/blog/ohbm-ondemand-how-to-resting-state-fmri-analysis
OHBM ONDEMAND HOW-TO: MACHINE LEARNING IN NEUROIMAGING
By Claude Bajada, Simon M. Hofmann and Ilona Lipp
Edited by: Thomas Yeo and Lisa Nickerson
Introduction
Machine learning, deep learning and artificial intelligence are terms that currently appear everywhere; in the media, in job adverts… and at neuroimaging conferences. Machine learning is often portrayed as a mystical black box that will either solve all our problems in the future or replace us in our jobs. In this blog post, we discuss what the term machine learning actually means, what methods it encompasses, and how these methods can be applied to brain imaging analysis. Doing this, we refer to the OHBM OnDemand material, which contains some great videos explaining machine learning methodology and we provide examples for how it has been used in a variety of applications. If you are curious about machine learning tools, but are not really sure whether you want to jump on the bandwagon, then we hope that this post is right for you and will help you get started.
See full content here: https://www.ohbmbrainmappingblog.com/blog/ohbm-ondemand-how-to-machine-learning-in-neuroimaging