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  • Oct 2019: A new Siemens PRISMA 3T MRI scanner will be installed in early 2020. This is funded by an SFI Infrastructure Grant.

Imaging Interest Group

Join the TCIN Imaging Interest Group (IIG) mailing list to receive the latest notifications.

Meetings are at 1.30pm on Thursdays in the Visualisation Room of the Lloyd Building (LB 2.01) unless otherwise stated.

10 Oct 2019 Laura Finnegan The School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin Manganese-enhanced MRI to asses optic nerve integrity in a mouse model of retinal degeneration.
4 Jul 2019 Judit Carrusta Centre for the Developing Brain, Kings' College London Early development of the brain functional architecture
6 Jun 2019 Oliviero Gobbo The School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin Development of a mouse model of glioblastoma for the study of local treatments, post-resection
23 May 2019 Vyacheslav (Slava) Karolis FMRIB, Oxford Structural and functional architectures in brain development and ageing.

13 May 2019
TCIN Third FloorSeminar Room (joint with NeuroSoc)

Jonathan Smallwood Psychology, The University of York The neural basis of on-going conscious experience
9 May 2019 John Butler School of Mathematical Sciences, TU Dublin Contradicting Neural Unreliability Thesis in Autism: Embracing the Null Hypothesis with Confidence
7 May 2019 Johann Kruschwitz Volition and Cognitive Control, Dresden University of Technology Graph theoretical modeling of brain connectivity: Concepts and workflow of brain connectivity analysis using graph theory.
28 Mar 2019 Dara Cannon Medicine, NUI Galway Psychiatry and the Human Connectome: Diffusion MRI Research Advances
14 Mar 2019 Alan Stone Biomedical Engineering, Trinity College Dublin Progressing quantitative MRI towards the clinic: Application of novel methods for insight into atherosclerosis, stroke, tumor and traumatic brain injury
28 Feb 2019 (joint with below) Evie Regan MEng Biomedical Engineering, University College Dublin Investigating the Deformation of the Masseter Muscle during Teeth Clenching and Grinding" and Dr. Catherine Jordan, a GBHI and Atlantic Fellow at TCD will be presenting: 'An fMRI pilot study exploring the influence of personally meaningful music on mild Alzheimer's Disease
28 Feb 2019 Catherine Jordan GBHI and Atlantic Fellow at Trinity College Dublin An fMRI pilot study exploring the influence of personally meaningful music on mild Alzheimer's Disease
31 Jan 2019 Erik O'Hanlon Trinity College Dublin and RCSI Imaging. What have you done for me lately?? What can your data do for you?


MRI Scanners

For human imaging, we have a 3T MRI. The scanner will be upgraded to a Siemens PRISMA in early 2020. The new scanner has:

  • much bettter signal-to-noise ratio, as the signal is digitised close the participant's head
  • stronger gradients (80 mT/m rather than 40 mT/m) for much better signal during diffusion MRI
  • faster scanning through simultaneous multi-slice functional MRI and diffusion MRI
  • force-compensated gradients to reduce vibration and noise, and methods for quieter scanning

For animal imaging, we have a small-bore 7 T MRI. This has:

  • a resolution of down to 25 microns (that's 0.025 mm)
  • a cryocoil for high signal-to-noise
  • three gradient sets (200-1000 mT/m) that trade off the diameter of the useable bore

Major Scientific Directions

Our centre is engaged in a wide range of imaging research, including for example:

  • Infant development: The development of the brain and mind in infants, and how they can be disrupted in infants from the neonatal intensive care unit.
  • Childhood MRI: The development of the brain in childhood, with a particular focus on autism, ADHD and psychosis.
  • Aging: How the brain changes through the lifespan, and early markers of dementia.
  • Brainstem function: How lesions to the brainstem affect the rest of the brain, and resulting behaviour.
  • In-vitro imaging: Arterial tissue mechanics, vascular imaging, vascular mechanobiology

MRI Acquisition Methods

Our teams measure many aspects of the brain:

  • Functional MRI: The activity in the brain evoked when a person watches or listens to something, or does a mental task.
  • Functional Connectomics: The connections between different brain regions, .
  • Diffusion MRI: A way to trace the white matter that connects different brain regions - the brain's wiring.
  • Structural MRI: The anatomy of the brain.

We study many populations:

  • Young adults: Many of our studies are conducted in university students
  • Older adults: To characterise how the brain changes through the lifespan.
  • Infants and children: To study how the brain and mind develop.
  • Autism and ADHD
  • Psychiatric populations
  • Disorders of consciousness
  • Neuropsychological patients with lesions of the cortex or subcortical regions

Analysis Methods

We have expertise in many areas of analysis:

  • Structural morphometry: assessing changes in brain structure (e.g., cortical thickness, lesions)
  • Functional MRI: measuring changes in brain activity, using volumetric and surface-based analyses
  • Functional Connectomics: measuring the connections between brain regions by examing correlated changes in activation
  • Tractography: tracing the connective tracts that join brain regions
  • Multi-voxel pattern analysis: analysing the patterns of brain activity evoked by different stimuli or tasks, through representational similarity analysis and decoding methods
  • Machine learning: using machine learning methods to classify activity or structrual chanes in the brain
  • Deep learning: testing computational models of brain function


Name Role and Group Interests Groups Primary acquisition methods Analysis methods
Alan Stone Postdoc in Lally Lab Developing new MRI methods to quantify physiology in the human body and translating these methods into the clinc Ex vivo vascular tissues, healthy volunteers and patients with carotid atherosclerosis Myelin Water Fraction, Mulit-compartment-T2, fMRI, ASL, calibrated fMRI, quantitative BOLD AFNI, FSL, matlab, python, shell scripting, pulse programming
Andrew Harkin PI Neuropharmacology, Animal models of CNS disorders, 7T imaging Animals, rats high res anatomical T2 weighted RARE, continuous arterial spin labelling FLASH, T1/T2 relaxation times MSME Paravision, ISA, IDL, Image J, MIPAV
Arun Bokde PI neuroimaging, neurodevelopment, depression, dementia healthy adults, neonates, prodromal Alzheimer's disease fMRI, DTI, MRI connectomme, tractography, network analysis, VBM
Brooke Tornifoglio PhD Researchers, Prof. Lally DTI, quantitative measures, ex vivo porcine carotid arteries, plaques obtained from endarterectomy patients DTI, T1, T2, DWI ExploreDTI, DSI Studio, FSL, MRtrix
Chiara Caldinelli PhD Candidate in Cusack Lab Infant neuroimaging Infants, healthy adults fMRI, DW-MRI
Christian Kerskens Lab assistant, lab manager, MRI technician, research follow, lead physicist, research lecturer, and principle investigator in TCIN quantum coherence, quantum biology healthy adults, locust, in vitro everything available tailored depending on project
Ciaran Conneely Operations Manager MRI operations across 3T and 7T      
Claire Gillan PI big data, psychiatry, prediction, habits, goal-directed control, antidepressant, machine learning healthy adults, mental health populations fMRI machine learning, computational modelling of reinforcement learning
Clare Kelly PI task, task-free, & naturalistic viewing analysis, big data, techniques and methods, programming children, adults, neurodevelopmental and psychiatric populations task, task-free, & naturalistic viewing, some DTI functional connectivity, inter-subject correlations, task-based analyses, mostly bash and matlab-based programming though expanding to r and python
Clíona O'Doherty Final year research project in Cusack lab Investigating how deep neural networks can help in Neuroimaging of the ventral visual stream Healthy adults N/A, project pending start Representational dissimilarity matrix
David Loane PI Traumatic brain injury, chronic neurodegeneration, dementia, neuroinflammation, pre-clinical animal models in vivo animal imaging - T2w, T1w/gadolinium, T2* Very basic - novice level (analysis was performed by collaborators)
Feng Deng PhD student in Naci lab brain mechanism, neuroimaging, machine learning/deep learning, computational modelling healthy midlife adults resting-state fMRI, task-based fMRI, DWI, sMRI, filed map, MRS, ASL GLM, ISC, ISFC, machine learning, deep learning methods
Kathy Ruddy RA in Neuropsychiatric Genetics Autism Lab Neuroimaging, EEG, Brain computer interface, stroke, MR-spectroscopy Healthy adults. Stroke patients DTI, fMRI, T1, rs-fMRI, MR-spectroscopy SPM for fMRI, Conn toolbox for rs-fMRI, ExploreDTI
Lorina Naci PI neuroimaging, cognition healthy participants, Alzheimer's patients, brain injury patients resting state fMRI, task-based fMRI, structural, DTI Matlab, SPM
Megan Ni Bhroin PhD Student in Bokde lab I'm interested in the functional network architecture of neonate encephalopathy patients. I use rs-fMRI to measure the resting state networks and use graph methods to quantify the global structure of the brain. I also plan to investigate the linear association between the functional connectome and inflammatory markers. Neonatal encephalopathy patients fMRI, dMRI
Nicola Taylor PhD student in Naci Lab Disorders of consciousness, Covert consciousness, fMRI Behaviourally non-responsive patients fMRI
Nigel Vahey Postdoc in Whelan lab Addiction; impulsivity; habits Not using fMRi yet. Work to date has focused upon EEG but I would like to learn more about designing/analysing fMRi research n/a n/a
Rhodri Cusack PI neurodevelopment; MRI acquisition and analysis methods infants fMRI (task and naturalistic), DWI, T1 matlab/SPM, python/FSL, freesurfer
Richard Carson PI human motor control; cognitive neuroscience; ageing; stroke; ALS healthy adults; stroke survivors; ALS patients diffusion weighted imaging; fMRI various "packages" (e.g. ExploreDTI) and custom routines (e.g. written in R, Matlab)
Richard O'Conaill Postdoc in Whelan lab Neurodevelopmental disorders, developmental cognitive neuroscience, clinical phenotyping, neural biomarkers Children and adolescents with neurodevelopmental disorders, individuals with rare genetic deletions associated with Autism and intellectual disability
Richard Reilly PI electrophysiology and MR based imaging of movement disorders. Active implantable devies and neuroimaging based objective measure for their evaluation Adult Dystonia patients and their adult relatives, healthy adults, Fragile X Permutation carriers, Cochlear Implant recipients, Adult Respiratory patients (asthma and COPD) VBM, Resting State, fMRI, DTI and keen to develop MR Spectrocopy skills Freesurfer and SPM. Matlab based analysis
Robert Johnston PhD researcher in Lally lab Atherosclerosis, Arterial Structure, Computational Biomechanics, Diffusion MRI Finite Element Analysis , Diffusion MRI ( ExploreDTI, DSIstudio, MRtrix) , Matlab.