Research

Facilities

MRI Centres

We have four major MRI research centres, which incorporate a range of MRI systems including:

Molecular Imaging Centres

We have four molecular imaging research centres, which incorporate a range of facilities including:

Further information about the SINAPSE Molecular Imaging group can be found within the Member Area (log-in required).

EEG / MEG / Neurostimulation

All our Imaging Centres have been equipped with fMRI compatible EEG from the same manufacturer. This facilitates comparison of data from multi-centre research trials.

Further information about cognitive neuroimaging in the SINAPSE Psychology group can be found within the Member Area (log-in required).

Optical Imaging

Vascular Assessment and Measurement Platform for Images of the REtina (VAMPIRE) is an international collaborative project of retinal image processing groups led by the Universities of Edinburgh and Dundee.

Ultrasound

Information about the SINAPSE Ultrasound group can be found within the Member Area (log-in required).

General enquiries about SINAPSE imaging facilities can be directed to Dr Kristin Flegal.

Funding

Postdoctoral and Early Career Researcher Exchanges (PECRE)

SINAPSE awards funding from SFC for enabling our early career researcher members to spend at least one month with partner organisations in Europe, North America, India or China.

Pools Engagement in European Research (PEER)

SINAPSE awards funding from SFC for supporting our members to participate in and compete for European funding.

Sources of imaging research funding in Scotland

Carnegie Trust

Royal Society of Edinburgh

Medical Research Scotland

Tenovus Scotland

Neurosciences Foundation

Chief Scientist Office

Other UK sources of imaging research funding

Biotechnology & Biological Sciences Research Council (BBSRC)

Engineering & Physical Sciences Research Council (EPSRC)

Medical Research Council (MRC)

Science & Technology Facilities Council (STFC)

Innovate UK

Wellcome Trust

Leverhulme Trust

Royal Society

National Institute for Health Research

Alzheimer's Research UK

Alzheimer's Society

British Heart Foundation

Stroke Association

Projects

SINAPSE members engage in imaging research projects at local, national, and international levels.

Highlighted below are ongoing major projects built on the strength of SINAPSE collaborations.

PET3D: PET Imaging in Drug Design and Development

An Innovative Training Network (ITN) funded (€4M) by the European Commission under the H2020 - MSCA-ITN-2015 programme, and coordinated by Prof Matteo Zanda at the University of Aberdeen.

IDentIFY: Improving Diagnosis by Fast Field-Cycling MRI

A Research and Innovation project funded (€6.6M) by the Horizon 2020 Programme and coordinated by Prof David Lurie at the University of Aberdeen.

ReDVA: Development of hemodynamic solutions in Renal Dialysis Venous Access

A Industry-Academia Partnerships and Pathways (IAPP) project funded (€2.6M) by the EU Seventh Framework Programme and coordinated by Prof Graeme Houston at the University of Dundee.

SVDs@Target: Small vessel diseases in a mechanistic perspective - Targets for intervention, affected pathways and mechanistic exploitation for prevention of stroke and dementia

A Research and Innovation project funded (€6M) by the Horizon 2020 Programme with Prof Joanna Wardlaw at the University of Edinburgh as a work package leader.

Understanding the role of the perivascular space in cerebral small vessel disease

A Transatlantic Networks of Excellence Program funded ($6M) by Fondation Leducq and coordinated by Prof Joanna Wardlaw at the University of Edinburgh.

Topic Groups

SINAPSE serves as the node for research imaging activity in Scotland, encompassing research across numerous disciplines using MRI, CT, PET, SPECT, EEG, MEG, ultrasound, and human optical imaging.

The breadth of expertise across imaging applications is balanced by ongoing activities within the following SINAPSE Topic Groups:

• Molecular Imaging
• Image Analysis
• Ultrasound
• Psychology
  

Molecular Imaging

SPECT: [123I]-beta-CIT uptake in the midbrain (arrows) showing the blocking of serotonin transporters by an antidepressant drug (Image credit: Dr Sally Pimlott, University of Glasgow)

The SINAPSE Molecular Imaging group brings together researchers whose work includes PET imaging, SPECT imaging, radiochemistry, and radiopharmacy.

Lead: Dr Sally Pimlott

Deputy Leads: Maria Clara Liuzzi and Kotryna Baronaite

• JISC Mailing List: SINAPSE-MI
• Further information for SINAPSE members: Member Area (log-in required)

Image Analysis

Retinal Imaging: Probability map of the retinal vasculature taken using an ultra widefield scanning laser ophthalmoscope (Image credit: Dr Tom MacGillivray, University of Edinburgh)

The SINAPSE Image Analysis group brings together researchers whose work includes processing, analysing, and developing software packages for medical imaging data.

Lead: Dr Gordon Waiter / Deputy Lead: Dr Islem Rekik

Student Lead: Emma Pead / Deputy Student Lead: Shaun Stone

• SINAPSE Software
  
• JISC Mailing List: SINAPSE-IA
• Further information for SINAPSE members: Member Area (log-in required)

Ultrasound

Ultrasound: Ex-vivo mouse aorta with branching left carotid and subclavian arteries (Image credit: Dr Carmel Moran, University of Edinburgh)

The SINAPSE Ultrasound group brings together researchers whose work includes medical ultrasound applications. Its members participate in meetings organised by the Scottish Ultrasound Group.

Lead: Prof George Corner

Deputy Lead: Conor MacDonald

• Further information for SINAPSE members: Member Area (log-in required)

Psychology

fMRI: Brain regions showing increased activation when expectations are violated in a memory test include fronto-parietal networks associated with cognitive control (Image credit: Dr Akira O’Connor, University of St Andrews)

The SINAPSE Psychology group brings together researchers who use imaging methods (including MRI, fMRI, EEG, and MEG) in Psychology research.

Lead: Dr Kristin Flegal

Deputy Lead: Dr Donald Lyall

• JISC Mailing List: SINAPSE-PSYCH
• Further information for SINAPSE members: Member Area (log-in required)

SINAPSE Software

DICOM Confidential

DICOM Confidential is an open source DICOM (Digital Imaging and Communications in Medicine) de-identification toolkit that provides the necessary flexibility to account for different de-identification requirements and does not impose a given anonymisation model. It also provides a mechanism for forwarding the anonymous output to a remote site using either SFTP (SSH File Transfer Protocol) or DICOM communications protocol. The core functionality is contained in a Java library, which we have used to develop two DICOM anonymisation applications; these are included in the toolkit: one for DICOM files contained in a folder and one for objects received via the DICOM protocol (a receiver). A separate graphical application is provided to help users in policy writing and configuration.

Origin: University of Edinburgh

Usage: Free, Open Source, Cross-platform

Tags:

• DICOM, Privacy protection

Posted by Dr. David Rodriguez

MCMxxxVI (1936) tool

Posted by Dr Maria Valdés Hernández

LIMO EEG

LIMO EEG is a Matlab toolbox (EEGLAB compatible) to analyse evoked responses over all space and time dimensions, while accounting for single trial variability using hierarchical linear modelling of the data. In addition, LIMO EEG provides robust parametric tests, therefore providing a new and complementary tool in the analysis of neural evoked responses. See Article

Origin: BRIC Edinburgh

Usage: Free, Open Source, Cross-platform

Tags:

• LIMO EEG, MEEG, Statistics

Posted by Dr Cyril Pernet

Online Research Tools

fMRI Tools

SINAPSE has created a protocol for fMRI quality assurance

• SINAPSE fMRI Quality Assurance Tutorial

For fMRI data processing, please see the Oxford FMRIB site or the CMU wiki

• http://www.fmrib.ox.ac.uk/
• http://imaging.mrc-cbu.cam.ac.uk/imaging/DesigningStudies

For statistical parametric mapping, please see

• http://www.fil.ion.ucl.ac.uk/spm/

Neuroimaging Tools

NITRC - Neuroimaging Informatics Tools and Resources Clearinghouse - is a resource bringing together various neuroimaging tools (for fMRI/MRI, EEG, MEG, CT, PET, SPECT, and optical imaging)

• http://www.nitrc.org/

BRAINS: Brain Images of Normal Subjects

Brain Images of Normal Subjects bank (http://www.brainsimagebank.ac.uk) is being developed with more than 1000 normal subjects from across the lifespan. It is collating images, and associated information (metadata) about health (e.g. blood pressure) already collected from people participating in research projects throughout Scotland. Many of these studies include detailed information from across the whole lifecourse, including socioeconomic status, current and previous health, medication use and cognitive ability tests. We are initially focussing on collecting data from studies at the extremes of life (old age and pre- and neo-natal) where there is most variability in brain structure, but we aim to expand the bank to include subjects of all ages.

The bank may be expanded in future to include subjects from other geographical locations, and patients with a range of neurological disorders, e.g. Alzheimer's disease, stroke, and schizophrenia.

The images have been collected in imaging centres across Scotland and are in a range of magnetic resonance (MR) sequences, including T1, T2, T2*, and fluid attenuated inversion recovery (FLAIR). When BRAINS is released these will be searchable by a wide range of metadata, e.g. blood pressure, age, MMSE.

BRAINS atlases are based on calculated distributions of brain structure rather than parametric estimates. These will be used to support image analysis research and clinical reporting of brain images.

Key publications and presentations

Development of Human Brain Image Banks and Age-Specific Normative Brain Atlases Workshop 28th-29th August 2014

Visiting students

Steering Committee

The BRAINS steering committee meets twice a year to discuss practical issues of setting up and maintaining the bank, and governance and ethical issues. The committee includes: Principal Investigators of the studies included in the bank (Alasdair MacLullich, Alison Murray, Susan Shenkin, Cyril Pernet, Roger Staff), Joanna Wardlaw, Mark Bastin, James Boardman, Jonathan Cavanagh, Fiona Denison, Ian Deary, Gordon Waiter) , people working on setting up the bank (David Dickie, Dominic Job, David Rodriguez Gonzalez), experts in ethics (Hester Ward) and law (Burkhard Schafer), and lay representatives.

Further Information

For further information please email Dr Susan Shenkin

VAMPIRE: Vascular Assessment and Measurement Platform for Images of the REtina

Vascular Assessment and Measurement Platform for Images of the REtina (http://vampire.computing.dundee.ac.uk) is a retinal image analysis software application and a collaborative project led by SINAPSE members from the University of Dundee and the University of Edinburgh.

Research tools created by VAMPIRE include annotation tools for Optic disc, Fovea, Junctions and Vessel Widths, and data from ultra-wide field-of-view fluorescein angriogram frames to which the VAMPIRE automatic vessel segmentation algorithm has been applied.

Key publications and presentations

Further information

For further information please email vampire_enquiries@dundee.ac.uk

Development of Human Brain Image Banks and Age-Specific Normative Brain Atlases

SFC SINAPSE SPIRIT Programme of Knowledge Exchange in Imaging

The keynote lecture  “Brain image banks: essential international research infrastructures for the 21st Century" will be delivered by Professor Paul Thompson, University of California, USA (LONI, ADNI) from 4.15pm to 5pm on the 28th August. Attendance at the keynote lecture is open to all.

Map of venue and further information available here

Suggested articles and resources for the meeting

Programme

Download programme as Word Document

BRAINS: Brain Images of Normal Subjects

Key Presentations and Publications

Pernet, C.R., Job, D.E., Wardlaw, J. M., Rodriguez, D.G

(2014) Sharing (non)personal data: the case of neuro-imaging. 'Dealing with Data' Conference and Research Data. The University of Edinburgh.

Dickie, D.A., Job, D.E., Sparrow, S., Piyasena, C., Wilkinson, G., Wardlaw, J.M., Boardman, J.P:

(Accepted). Preterm infant brain pathology revealed in individuals by voxel ranking against a normal term atlas. Proceedings of the 20th Annual Meeting of the Organization for Human Brain Mapping. Hamburg, Germany.

Dickie, D.A., Job, D.E., Wardlaw, J.M., Laidlaw, D.H., Bastin, M.E:

(2014) Evidence of non-normal distributions in brain imaging data from normal subjects: implications for diagnosis of disease. Proc. Intl. Soc. Mag. Reson. Med. 22.

Article by Dr Susan Shenkin in The Conversation 17 June 2013 - Brain scan library will help us understand normal ageing.

Dickie, D.A., Job, D.E., Rodríguez González, D., Shenkin, S.D., Ahearn, T.S., Murray, A.D., Wardlaw, J.M:

(2013). Variance in brain volume with advancing age: implications for defining the limits of normality.PLOS ONE.

(2013). How normal is this brain? Development and testing of a new MR template for voxel–based brain ranking. Proceedings of the 19th Annual Meeting of the Organization for Human Brain Mapping. Seattle, USA.

(2013). Development of automatic, voxel–based brain ranking. Anne Rowling Regenerative Neurology Clinic launch meeting. Edinburgh, UK.

(2013). Brain Images of Normal Subjects (BRAINS) Bank. NHS Lothian Annual Research Conference. Edinburgh, UK. Poster Competition First Prize.

(2013). How normal is this brain? A new nonparametric voxel-based method of comparing brain scans to age-appropriate reference templates. British Geriatrics Society Autumn Meeting. Harrogate, United Kingdom.

(2012). Distinguishing normal and pathological ageing brain structures with data not statistics. CCACE 5th Annual Research Day. Edinburgh, UK. Young Scientist Poster Award.

(2012). A databank, rather than statistical, model of normal ageing brain structure to indicate pathology.Proceedings of the 18th Annual Meeting of the Organization for Human Brain Mapping. Beijing, China.Guarantors of Brain Travel Award.

Dickie, D.A., Job, D.E., Poole, I., Ahearn, T.S., Staff, R.T., Murray, A.D., Wardlaw, J.M:

(2012). Do brain image databanks support understanding of normal ageing brain structure? A systematic review Eur Radiol. 22 (7), 1385–1394. Received editorial: Barkhof, F. (2012). Making better use of our brain MRI research data.

Rodríguez González, D., Job, D.E., Dickie, D.A., Shenkin, S.D., Wardlaw, J.M:

(2012). Integrating Data Sharing and Data Curation in a Normative Brain Imaging Bank. International Digital Curation Conference. Amsterdam, Netherlands:

Poline JB1, Breeze JL, Ghosh S, Gorgolewski K, Halchenko YO, Hanke M, Haselgrove C, Helmer KG, Keator DB, Marcus DS, Poldrack RA, Schwartz Y, Ashburner J, Kennedy DN.

(2012) Data sharing in neuroimaging research. Frontiers in Neuroinformatics

Paper by Dr C. Farrell and colleagues in European Radiology, 2009 - Development and initial testing of normal reference MR images for the brain at ages 65-70 and 75-80 years

Development of Human Brain Image Banks and Age-Specific Normative Atlases (28th-29th August)

SFC SINAPSE SPIRIT Programme of Knowledge Exchange in Imaging

Information for Delegates

The conference will be held at the Royal Society of Edinburgh, 22-26 George St, Edinburgh, EH2 2PQ. The Royal Society of Edinburgh is Scotland's National Academy of Science & Letters. It is an independent body with charitable status, established in 1783. It is located in the heart of the city, a short walk from Waverley train station.

The centre of Edinburgh consists of the Old Town, the main artery of which is called the Royal Mile and runs from the Castle to Holyrood Palace, and the neoclassical and Georgian New Town built between 1765 and 1850. The Old and New Towns are a designated UNESCO World Heritage Site.

August is the busiest time in the Edinburgh Festival calendar. During your visit there will be events from the International Festival, the Art Festival, and the Mela Festival of world music and dance.

The List is the most well-established listings magazine and website for central Scotland covering cinema, theatre, music, comedy, and places to eat and drink.

Visit Scotland is the website of Scotland's national tourism organisation.

Many thanks to our funders whose contributions have made this meeting possible:

Development of Human Brain Image Banks and Age-Specific Normative Brain Atlases

SFC SINAPSE SPIRIT Programme of Knowledge Exchange in Imaging

Instructions for different roles for Brain Image Bank Workshop

1) Speaker in introductory session:

A FIVE MINUTE summary of the brain image banks/atlases you are part of. We are trying to cover a wide range of existing and emerging resources in the first session (10 talks) in a limited  time, so could  you please limit your talk to 5 slides maximum, and cover: the population/sample that you cover, the structure and main  uses of your bank(s), the main challenges you have had and how these  have been overcome; and what you see as future opportunities or  challenges for brain image banking.

We aim to have time for general discussion of the issues arising after all the presentations.

2) Speaker for individual sessions (Evans, Laurie, Poline, Smith)

A TEN MINUTE summary of the main issues relating to the topic. If there are particular issues you would like to highlight to Chairs in the discussion session or you have any key references or resources (that you haven't already shared) please let Dr Susan Shenkin know.

The meeting will then be split into three groups (these will be allocated) to discuss the individual topics. Each group (20-25 people) will have a Chair (named in the programme), Scribe and Spokesperson (will be allocated).

3) Chair for discussion topic groups

You are not required to give a talk, but we would like you to help steer the discussion towards considering the main issues that concern your topic. We are aiming for 45 minutes of discussion, and 15 minutes of feedback per topic. You are of course welcome to liaise with the speaker introducing your session directly, or I can put you in contact. Don’t feel restricted to what we have suggested in the programme. We would like you to guide this international group of experts and practitioners to come up with two or three main points to discuss, and then a list of options of how to address these points (or which points need further exploration or work) and ideally an order of priority, and preferred option for each item discussed. This will then be fed back to the whole workshop through a moderated discussion to try and reach a conclusion on how to take these issues forward. We aim to produce a paper summarising the proposals.

In summary, we are asking you just to consider which are the main issues you think should be discussed and to guide the group in coming up with their suggestions and solutions.

We will allocate a scribe to keep track of the discussion, working with a spokesperson if necessary to feedback to the main group.

4) Feedback discussion moderator

You will chair the opening talk and also coordinate the feedback of decisions arrived at by each discussion group, clarifying the main issues raised by each group and seeking additional comments/suggestions/solutions from the whole meeting (2/3 of which will have been in another session). Please try and watch the time so that all the topics are covered in the session.

5) Others

Thanks for participating in the workshop. Although you don’t have an allocated role on the programme, we are hoping everyone will take an active role in the meeting and discussions. We will allocate you to a discussion group for each session, and many of you will be allocated as either Scribe or Spokesperson for one of the sessions.

Development of Human Brain Image Banks and Age-Specific Normative Atlases (28th-29th August)

SFC SINAPSE SPIRIT Programme of Knowledge Exchange in Imaging

Resources pack for Brain Image Bank and Brain Atlas Workshop

(see http://tinyurl.com/qzokcfn for updates and links to online abstracts/articles)

Download this resource pack as a Word Document

Session 1: Current and emerging brain image banks and atlases

a) MNI: Alan Evans

• Evans AC, Janke AL, Collins DL, Baillet S. Brain templates and atlases Neuroimage. 2012 Aug 15;62(2):911-22. doi: 10.1016/j.neuroimage.2012.01.024.

• K Amunts et al, BigBrain: An Ultrahigh-Resolution 3D Human Brain Model Science 2013: Vol. 340 no. 6139 pp. 1472-1475 DOI: 10.1126/science.1235381

• S Das, AP Zijdenbos, J Harlap, D Vins, AC Evans LORIS: a web-based data management system for multi-center studies Front Neuroinform. 2011; 5: 37. doi: 10.3389/fninf.2011.00037

b) ENIGMA: Paul Thompson

• ENIGMA Consortium Website http://enigma.ini.usc.edu

• ENIGMA Consortium - Video: http://www.youtube.com/watch?v=VZbxLbzN5vk

• Thomspon P et al. The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data Brain Imaging Behav. 2014; 8: 153–182. doi: 10.1007/s11682-013-9269-5; http://enigma.ini.usc.edu/wp-content/uploads/2014/01/Thompson_ENIGMA_Consortium_BIBreview.pdf

c) GIN: Bernard Mazoyer

• http://www.three-city-study.com; http://www.i-share.fr/frontpage

• http://www.gin.cnrs.fr/?lang=en

• http://www.i-share.fr/frontpage

• 3C study group (2003) Vascular factors and risk of dementia: design of the Three-City Study and baseline characteristics of the study population. Neuroepidemiology 22 :316-325.

• Dufouil C, Chalmers J, Coskun O, Besancon V, Bousser MG, Guillon P, MacMahon, S, Mazoyer B, Neal B, Woodward M, Tzourio-Mazoyer N, Tzourio C (2005); PROGRESS MRI Substudy Investigators. Effects of blood pressure lowering on cerebral white matter hyperintensities in patients with stroke: the PROGRESS (Perindopril Protection Against Recurrent Stroke Study) Magnetic Resonance Imaging Substudy. Circulation 12:1644-50.

• Lemaitre H, Crivello F, Grassiot B, Alperovitch A, Tzourio C, Mazoyer B (2005). Age- and sex-related effects on the neuroanatomy of healthy elderly. Neuroimage 26:900-911.

• Stewart B, Dufouil C, Godin O, Ritchie K, Maillard P, Delcroix N, Crivello F, Mazoyer B, Tzourio C (2008) Neuroimaging correlates of subjective memory deficits in a community population. Neurology 70:1601-1607.

• Crivello F, Lemaitre H, Dufouil C, Grassiot B, Delcroix N, Tzourio-Mazoyer N, Tzourio C, Mazoyer B (2010). Effects of ApoE-ε4 allele load and age on the rates of grey matter and hippocampal volumes loss in a longitudinal cohort of 1,186 healthy elderly persons. Neuroimage 53:1064-1069.

• Kurth T, Mohamed S, Maillard P, Zhu YC Chabriat H, Mazoyer B, Bousser MG, Dufouil C, Tzourio C (2011) Headache, Migraine, and Structural Brain Lesions and Function: population-based EVA MRI Study. British Medical Journal Jan 18;342:c7357.

• Stewart B, Godin O, Crivello F, Maillard P, Mazoyer B, Tzourio C, Dufouil C (2011) Longitudinal neuroimaging correlates of subjective memory impairment in a 4-year prospective community study. British Journal of Psychiatry 198:199-205.

• Tzourio-Mazoyer N, Marie D, Zago L, Perchey G, Leroux G, Mellet E, Jobard G, Joliot M, Crivello F, Petit L, Mazoyer B (2014) Heschl’s gyrification pattern is related to speech listening hemispheric lateralization fMRI investigation in 281 healthy volunteers. Brain Structure and Function (epub March 18)

d) INCF/IMAGEN: Jean-Baptiste Poline

• http://www.incf.org/documents/workshop-reports/towards-a-multi-modal-human-brain-atlas;

• http://www.incf.org/documents/incf-at-a-glance

• Poline JB, Breeze JL, Ghosh S, Gorgolewski K, Halchenko YO, Hanke M, Haselgrove C, Helmer KG, Keator DB, Marcus DS, Poldrack RA, Schwartz Y, Ashburner J, Kennedy DN. (2012) Data sharing in neuroimaging research. Frontiers in Neuroinformatics 2012 | doi: 10.3389/fninf.2012.00009 http://journal.frontiersin.org/Journal/10.3389/fninf.2012.00009/abstract

e) OASIS/HCP: Dan Marcus

• https://db.humanconnectome.org; https://www.oasisbrains.org

• http://www.xnat.org

f) BRAINS: Susan Shenkin

• Dickie, D.A., Job, D.E., Wardlaw, J.M., Laidlaw, D.H., Bastin, M.E:(2014) Evidence of non-normal distributions in brain imaging data from normal subjects: implications for diagnosis of disease. Proc. Intl. Soc. Mag. Reson. Med. 22.

• Dickie, D.A., Job, D.E., Rodríguez González, D., Shenkin, S.D., Ahearn, T.S., Murray, A.D., Wardlaw, J.M:(2013). Variance in brain volume with advancing age: implications for defining the limits of normality .PLOS ONE 8(12): e84093. DOI: 10.1371/journal.pone.0084093

• Dickie, D.A., Job, D.E., Poole, I., Ahearn, T.S., Staff, R.T., Murray, A.D., Wardlaw, J.M: (2012). Do brain image databanks support understanding of normal ageing brain structure? A systematic review Eur Radiol. 22 (7), 1385–1394. Received editorial: Barkhof, F. (2012). Making better use of our brain MRI research data.

• Farrell C, Chappell F, Armitage PA, Keston P, MacLullich A, Shenkin S, Wardlaw JM. European Radiology, 2009; 19(1):177-183 - Development and initial testing of normal reference MR images for the brain at ages 65-70 and 75-80 years

g) EPI2: Rotterdam/Leiden: Aad van der Lugt

• www.populationimaging.eu

• MA Ikram, A van der Lugt, WJ Neissen, GP Krestin, PJ Koudstaal, A Hofman, MMB Breteler, MW Vernnoij The Rotterdam Scan Study: design and update up to 2012 Eur J Epidemiology (2011) 26: 811-824

h) Rhineland: Monique Breteler

• http://www.dzne.de/en/research/research-areas/population-studies.html

i) Biobank: Steve Smith

• http://www.ukbiobank.ac.uk/

• http://imaging.ukbiobank.ac.uk/imaging.html

j) UK Dementia Platform: Clare Mackay (see resources in folder, UKDP and MIRIAD slide)

• http://www.mrc.ac.uk/research/facilities/dementias-research-platform/

k) Perinatal banks: James Boardman

• Serag A, Aljabar P, Ball G, Counsell SJ, Boardman JP, Rutherford MA, Edwards AD, Hajnal JV, Rueckert D. Construction of a consistent high-definition spatio-temporal atlas of the developing brain using adaptive kernel regression. Neuroimage. 2012 Feb 1;59(3):2255-65

• Bassi L, Chew A, Merchant N, Ball G, Ramenghi L, Boardman J, Allsop JM, Doria V, Arichi T, Mosca F, Edwards AD, Cowan FM, Rutherford MA, Counsell SJ. Diffusion tensor imaging in preterm infants with punctate white matter lesions. Pediatr Res. 2011 Jun;69(6):561-6.

• Kuklisova-Murgasova M, Aljabar P, Srinivasan L, Counsell SJ, Doria V, Serag A, Gousias IS, Boardman JP, Rutherford MA, Edwards AD, Hajnal JV, Rueckert D. A dynamic 4D probabilistic atlas of the developing brain. Neuroimage. 2011 Feb 14;54(4):2750-63

Resources from Serena Counsell’s group:

• http://www.kcl.ac.uk/medicine/research/divisions/imaging/centres/cdb/index.aspx

Resources from Petra Hüppi’s group (Lana Vasung):

• Dubois J, Benders M, Cachia A, Lazeyras F, Ha-Vinh Leuchter R, Sizonenko SV, Borradori-Tolsa C, Mangin JF, Hüppi PS. Mapping the early cortical folding process in the preterm newborn brain. Cereb Cortex. 2008 Jun;18(6):1444-54. http://cercor.oxfordjournals.org/content/18/6/1444.long

• Fischi-Gómez E¹, Vasung L, Meskaldji DE, Lazeyras F, Borradori-Tolsa C, Hagmann P, Barisnikov K, Thiran JP, Hüppi PSStructural Brain Connectivity in School-Age Preterm Infants Provides Evidence for Impaired Networks Relevant for Higher Order Cognitive Skills and Social Cognition. Cereb Cortex. 2014 May 2. [Epub ahead of print] http://cercor.oxfordjournals.org/content/early/2014/05/02/cercor.bhu073.long

• Gui L, Lisowski R, Faundez T, Hüppi PS, Lazeyras F, Kocher M. Morphology-driven automatic segmentation of MR images of the neonatal brain. Med Image Anal. 2012 Dec;16(8):1565-79. doi: 10.1016/j.media.2012.07.006. Epub 2012 Jul 31. http://www.sciencedirect.com/science/article/pii/S1361841512000989

• Kunz N, Zhang H, Vasung L, O'Brien KR, Assaf Y, Lazeyras F, Alexander DC, Hüppi PS.Assessing white matter microstructure of the newborn with multi-shell diffusion MRI and biophysical compartment models.Neuroimage. 2014 Aug 1;96:288-99. doi: 10.1016/j.neuroimage.2014.03.057. Epub 2014 Mar 28. http://www.sciencedirect.com/science/article/pii/S1053811914002183

• Kwon SH, Vasung L, Ment LR, Huppi PS.The role of neuroimaging in predicting neurodevelopmental outcomes of preterm neonates. Clin Perinatol. 2014 Mar;41(1):257-83. doi: 10.1016/j.clp.2013.10.003. Epub 2013 Dec 12. http://www.sciencedirect.com/science/article/pii/S0095510813001292

• van de Looij Y, Vasung L, Sizonenko SV, Hüppi PS. MRI of animal models of developmental disorders and translation to human imaging. Curr Opin Neurol. 2014 Apr;27(2):157-67. doi: 10.1097/WCO.0000000000000066

Session 2 "What is normal?": Alan Evans

• Wachbroit R. Normality as a biological concept. Philosophy of Science 1994;61:579-591 http://www.jstor.org/stable/188336

Discussion groups:

1. Minimum image and metadata to define normality (John Ashburner)

2. How to use existing data, likely gaps (Monique Breteler)

3. Combining all stages of life in one image bank (James Boardman/Dominic Job)

Session 3 "Legal and ethical issues" Grahame Laurie

Discussion groups:

1. Consent, industry, international issues (Burkhard Schaefer)

2. Privacy, anonymisation, levels of access (Hester Ward)

3. Research tourism, incidental findings (Alison Murray)

• Schmidt CO, Hegenscheid K, Erdmann P, Kohlmann T, Langanke M, Völzke H, Puls R, Assel H, Biffar R, Grabe HJ. Psychosocial consequences and severity of disclosed incidental findings from whole-body MRI in a general population study. European Radiology, May 2013, Volume 23, Issue 5, pp 1343-1351

Session 4 Multisource 'big' data: "What do we need to use big data" JB Poline

• JB Poline, JL. Breeze, St Ghosh, KGorgolewski, YO Halchenko, M Hanke, C Haselgrove, K G. Helmer, DB. Keator, DS Marcus, RA Poldrack, Y Schwartz, J Ashburner DN Kennedy - Data sharing in neuroimaging research Front. Neuroinform., 2012 | doi: 10.3389/fninf.2012.00009

http://journal.frontiersin.org/Journal/10.3389/fninf.2012.00009/abstract

• Poline, JB, and RA Poldrack. Introduction to the Special Issue: Toward a New Era of Databasing and Data Sharing for Neuroimaging. NeuroImage 82, (2013): 645–46. http://www.sciencedirect.com/science/article/pii/S1053811913009075

• Open access: Practical costs of data sharing Geoffrey J. Goodhill Nature 509, 33 (30 April 2014) | doi:10.1038/509033b http://www.nature.com/nature/journal/v509/n7498/full/509033b.html and reply Steve Eglan http://www.nature.com/nature/journal/v510/n7505/pdf/510340c.pdf

Discussion groups:

1) Harmonising data (Aziz Sheikh)

• Lynch, C. (2008) Big data: How do your data grow? Nature 455, 28-29

• K Amunts, MJ Hawrylycz, DC Van Essen, JD Van Horn, N Harel, J-B Poline, F De Martino, JG Bjaalie, G Dehaene-Lambertz ,S Dehaene, P Valdes-Sosa, B Thirion, K Zilles, SL Hill, MB Abrams, PA Tass, W Vanduffel, AC Evans, SB Eickhoff, Interoperable atlases of the human brain NeuroImage.2014, 99: 525–532; DOI: 10.1016/j.neuroimage.2014.06.010

2) Database Infrastructure (Dan Marcus)

3) Data provenance, quality assurance (Albert Burger)

• W3C PROV: Provenance Current Status: http://www.w3.org/standards/techs/provenance#w3c_all

• EDBT/ICDT 2013 (http://www.edbt.org/Proceedings/2013-Genova/edbt_toc.html) Missier P, Belhajjame K, Cheney J. The W3C PROV family of specifications for modelling provenance metadata, EDBT '13 Proceedings of the 16th International Conference on Extending Database Technology p773-776, http://www.edbt.org/Proceedings/2013-Genova/papers/edbt/a80-missier.pdf

• ACM Practice: A Primer on Provenance http://cacm.acm.org/magazines/2014/5/174341-a-primer-on-provenance/fulltext

• AJ MacKenzie-Graham, JD Van Horn, R P Woods, KL Crawford, AW Toga Provenance in NeuroimagingNeuroimage. Aug 1, 2008; 42(1): 178–195. doi: 10.1016/j.neuroimage.2008.04.186

• AW Toga Neuroimage databases: The good, the bad and the ugly Nature Reviews Neuroscience 3, 302-309 (April 2002) | doi:10.1038/nrn782

• JB Poline, JL. Breeze, St Ghosh, KGorgolewski, YO Halchenko, M Hanke, C Haselgrove, K G. Helmer, DB. Keator, DS Marcus, RA Poldrack, Y Schwartz, J Ashburner DN Kennedy - Data sharing in neuroimaging research Front. Neuroinform., 2012 | doi: 10.3389/fninf.2012.00009 http://journal.frontiersin.org/Journal/10.3389/fninf.2012.00009/abstract

Session 5 Making image databanks work: Steve Smith

1) Atlas creation tools and registration issues (variability) (Bernard Mazoyer)

2) Data sharing/citation/storage (Steve Pavis and David Wyper)

• EE Wilhelm, E Oster, I Shoulson. Approaches and Costs for Sharing Clinical Research Data JAMA. Published online February 20, 2014. doi:10.1001

• S Schneeweiss Learning from Big Health Care Data N Engl J Med 2014;370:2161-2163/jama.2014.850

• R Kush, M Goldman Fostering Responsible Data Sharing through Standards N Engl J Med 2014;370:2163-2165

• BM Psaty and AM Breckenridge Mini-Sentinel and Regulatory Science - Big Data Rendered Fit and Functional N Engl J Med 2014;370:2165-2167

Other general useful resources:

• G Ziegler, GR Ridgway, R Dahnke, C Gaser, for The Alzheimer's Disease Neuroimaging Initiative Individualized Gaussian process-based prediction and detection of local and global gray matter abnormalities in elderly subjects NeuroImage, Vol 97, 15 August 2014, P 333–348, ^a Wellcome Trust Center for Neuroimaging, Institute of Neurology, London, UK. DOI: 10.1016/j.neuroimage.2014.04.018

• MIRIAD: Minimal Interval Resonance Imaging in Alzheimer's Disease (Nick Fox)

46 clinical AD, 23 age‐matched elderly controls, Longitudinal (up to 12 scans) volumetric MRI scanning on single 1.5T scanner http://www.ucl.ac.uk/drc/research/miriad/Database

• G Neil Roberts: Guo et al Towards an elastographic atlas of brain anatomy PLOSOne 2013 DOI: 10.1371/journal.pone.0071807 (in file)

• Cresswell, KM; Bates, DW; Sheikh, A, Ten key considerations for the successful implementation and adoption of large-scale health information technology. J Am Med Inform Assoc, 2013 vol. 20(e1) pp. e9-e13. PMID: 23599226. PMCID: PMC3715363

• J. B. Poline, R. A. Poldrack, Introduction to the special issue: Towards a new era of databasing and datasharing for neuroimaging. NeuroImage, Vol 82, 15 November 2013, pp645-646.

Many thanks to our funders whose contributions have made this meeting possible:

BRAINS: Brain Images of Normal Subjects

Eilidh Edmiston was a visiting student on the BRAINS project in summer 2015, as part of a Nuffield Research Placement (http://www.nuffieldfoundation.org/nuffield-research-placements). She piloted and adapted a questionnaire to understand how clinicians use brain image templates, which will inform a wider online survey.

Eilidh presenting her poster at the Royal College of Physicians of Edinburgh.

Juyoung Lee and Daniel Taylor were visiting students on the BRAINS project in summer 2014.

Juyoung conducted a systematic review of structural brain MRI atlases. This review documented the subjects and methods used to create structural brain MRI atlases. Initial results show that older subjects (>60 years) were often under-represented and that parametric methods were most commonly used to combine individual images into an atlas.

Daniel developed a questionnaire to aid design of a brain MRI atlas interface for supporting radiological diagnoses in individual patients. The questionnaire assessed user preferences and specific features that would be useful in clinical versus research environments. Daniel completed pilot testing of the questionnaire and it will soon be mass distributed electronically to mailing lists of clinicians and researchers.

Postdoctoral and Early Career Researcher Exchanges (PECRE)

The main purpose of PECRE funding is to provide research training and development opportunities for the most able postgraduate and early career researcher members of SINAPSE, while at the same time building experience of international collaboration with academia and/or industry.

This funding is available only to SINAPSE members who belong to one of the seven partner Universities: Aberdeen, Dundee, Edinburgh, Glasgow, St. Andrews, Stirling, and Strathclyde.

Conditions of award

• Each candidate may be the recipient of a single award only, up to a maximum value of £7,500. (Note however that one award can cover visits to multiple institutions or multiple visits to the same institution.)

• Each exchange must be for a minimum period of at least one month. (Note however that multiple visits for periods of less than one month each are permissible.)

• The funding must be used to support exchanges in Europe (outwith the UK), North America, China, and India only.

• Eligible costs are restricted to economy travel and subsistence at the agreed institutional rate. Research costs are not eligible, and the funding must not be used for attendance at conferences, training seminars and the like.

Applications for PECRE funding are currently being accepted for exchanges in academic year 2017-18 or 2018-19. The application form can be downloaded here, and must be submitted by the deadline of 27 April 2018 for consideration in this round.

Enquiries can be directed to kristin.flegal@glasgow.ac.uk.

Past awards

PECRE funding has been awarded in these previous rounds of applications:

• Round 6 (2017-2018)
  
• Round 5 (2016-2017)
• Round 4 (2015-2016)
• Round 3 (2014-2015)
• Round 2 (2013-2014)
• Round 1 (2012-2013)

Click below to explore an interactive map showing the exchange destinations for previous SINAPSE recipients of PECRE funding:

Pools Engagement in European Research (PEER)

The main purpose of PEER funding is to support SINAPSE members in engaging with European research, for example through establishing network connections, showcasing our pool’s skills and capabilities and participating in specific networking activities both for policy influencing and project preparation, in addition to developing proposals and applying for funding under the European Framework Programme.

This funding is available only to SINAPSE members who belong to one of the seven partner Universities: Aberdeen, Dundee, Edinburgh, Glasgow, St. Andrews, Stirling, and Strathclyde.

Eligible costs include:

• Travel and subsistence (at the agreed institutional rate) for attendance at networking events or consortium meetings.
• Grant writing consultation.
• Staff time or services employed specifically for EU partnership building.

European research proposals involving partnerships with Scottish SMEs are encouraged, however the funding must not be used for partner organisations' travel or subsistence costs.

Applications for PEER funding can be submitted at any time. Enquiries can be directed to kristin.flegal@glasgow.ac.uk.

Congratulations to SINAPSE recipients of PECRE funding for international research exchanges

Round 6 (2017-2018)

• 1st tranche
• 2nd tranche

Round 5 (2016-2017)

Round 4 (2015-2016)

• Ellen Backhouse visited the University of Amsterdam in the Netherlands for a project investigating the effect of malnutrition during gestation on later life health - focusing on cerebral small vessel disease burden, assessed using MRI markers, and depression - in the Dutch Famine Birth Cohort.
• Ellen describes her research on early life risk factors for stroke in a 3-minute video here!
  

• Benjamin Dering visited the Catholic University of the Sacred Heart in Milan, Italy to learn a new technique used in animal studies, single cell patch clamp electrophysiology, which has complemented his existing human neuroimaging work by enabling him to study electrophysiological signals that may be comparable between animal and human models.

• Simon Ladouce visited the University of Oldenburg in Germany and Brussels University in Belgium to learn from leading groups in the emerging field of mobile EEG, which allowed him to develop technical expertise including specialised signal processing and analysis methods for addressing challenges unique to mobile EEG recordings such as motion-related noise.
• Simon describes his mobile EEG research in a 3-minute video here!

• Conor MacDonald visited the imaging contrast agent manufacturer Guerbet in Paris, France for a joint industry-academia project involving MRI and CT contrast agent applications.

• Jamie Murray visited Humboldt University and the Max Planck Institute in Berlin, Germany to learn a new method for correcting latency variability in EEG event-related potentials using single trial analysis, which he has applied to data from a study of ageing and memory for a more reliable comparison of neural data between older and younger adults.

• Monica Piras visited the Fondazione IRCCS Istituto Nazionale dei Tumori in Milan, Italy to develop tumour xenograft mouse models for in vivo evaluation of novel molecular imaging probes.

• Laura Young visited the imaging contrast agent manufacturer Guerbet in Paris, France for a joint industry-academia project investigating the safety and efficacy of gadolinium-based MRI contrast agents.

Round 3 (2014-2015)

• Eric Barnhill visited the Charité - Universitätsmedizin in Berlin, Germany for a project investigating the the sensitivity of Magnetic Resonance Elastography (MRE) for detecting age related changes in brain tissues.

• Bharath Kumar Cheripelli visited Aarhus University in Denmark for a project evaluating capillary transit time heterogeneity (CTTH) as an image analysis technique for mapping of core and penumbra in acute ischemic stroke.

• Samuel Danso visited Harvard Medical School in Massachusetts, USA to develop analytical tools for application to BRAINS imagebank linked data and other imaging databases being developed by SINAPSE researchers.

• Anna Heye visited Oregon Health & Science University in Oregon, USA, Copenhagen University in Denmark, and University Hospital Rome in Italy for a project investigating dynamic contrast-enhanced MRI image analysis and modeling approaches.

• Dominic Job visited McGill University in Montreal, Canada, UCLA in California, USA, Washington University in Missouri, USA, and Commissariat à l'Energie Atomique in France to improve the infrastructure and sustainability of the BRAINS imagebank and ensure compatibility with established international banks to allow integration of images and phenotypic data.

• Cyril Pernet visited Toulouse Cedex in France for a project integrating the LIMO EEG toolbox he developed for the statistical analysis of EEG data with EEGLAB software.
  

Round 2 (2013-2014)

• Dorota Chapko visited UCSF in California, USA to learn neuroimaging data modelling techniques relevant to life-course research.

• Panos Lepipas visited the TRIUMF National Laboratory for Particle and Nuclear Physics in Vancouver, Canada for a project involving medical radioisotope production using next generation laser wakefield accelerators.

• Islem Rekik visited Johns Hopkins University in Maryland, USA to develop computational models of changes in brain imaging data.

Round 1 (2012-2013)

• Sergio Dall'Angelo visited Harvard University in Massachusetts, USA to study a 'late-stage' fluorination process holding promise to revolutionise the field of PET radiofluorination.

• David Dickie visited McGill University in Montreal, Canada, UCLA in California, USA, and Washington University in Missouri, USA, for a project developing a 'living brain bank' using MR images of normal subjects already acquired as part of research projects across SINAPSE.

• Andreas Glatz visited Medical University Graz in Austria to develop MRI sequences to analyse basal ganglia iron deposits that are putative biomarkers for cognitive aging and small vessel disease.

• Dima Maneuski visited the University of Liège in Belgium for a project evaluating the medipix detector for use in radioisotope generators.

• Ravi Mill visited Washington University in Missouri, USA, to learn a new technique, infrared eye-tracking, which instilled his primary research interest of exploring multiple neuroimaging modalities in the study of cognition.
  

• Meg Pajak visited University of Valencia in Spain and Notre Dame University in Indiana, USA to develop expertise in micro-SPECT-PET-CT image acquisition, protocol development, and performance assessment.

• Joanne Park visited the Center for the Neural Basis of Cognition in Pennsylvania, USA to learn fMRI techniques which complemented her existing Event-Related Potential (ERP) work in human memory research.