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UCL Centre for Doctoral Training in Medical Imaging

Critical Review of Key Papers in Biomedical Imaging (The Journal Club)

Course Information

    Course Credits: 15 (MPHYGB25, first and second term)   

    Assessment: Presentation, Class Contribution and Coursework

    Course Organisers: Dr Andrew MelbourneDr Tammy KalberDr Ivana Drobnjak

Aims and Objectives

Understanding and forming an accurate opinion of a journal article is a crucial skill for research; the DTP Journal Club aims to equip students with the skills necessary to carry out a critical review of literature relevant to their field.

Students will work together through group work and discussion to develop skills for critical thinking and reviewing, and understand the motivation for paper writing whilst developing academic presentation skills.

Class Structure

In 2014/2015 the DTP MRes students, each week in rotation, will present a paper chosen by an academic member of staff who will then chair the session. The format will be a 10 minute presentation by the lead presenter describing the aims and motivation for the work the methodology and the results. After group-based discussion of these sections, this will be followed by two further 5 minute presentations by two members of the group which will describe in detail the contributions and limitations of the paper. This will be followed by discussion on these sections and on the impact of the paper. The academic chairperson will help guide the discussion. Written reviews will be due in approximately half-way through the course and at the end of the student rotation.

In 2014/2015 sessions are likely to last about 90minutes.

Assessment and Feedback

Students will be assessed in three categories:

Presentation Skills: Each student will present three times during the rotation, once as lead presented and once each presenting the contributions and limitations of the paper. Students will be assessed on each presentation. Students will be assessed on their general presentation skills, strength of conclusions and ability to handle questions.

Class Contribution (throughout the year): Students will be expected to contribute to the class throughout the year by raising questions, contributing to the discussion and voicing opinions. Attendance will form a component of class contribution.

Individual Paper Review (twice during the rotation): Students will be asked to submit a written review of one of the papers from the first and second half of the paper rotation. The review should summarise the paper and reflect upon contemporary literature. In the case of older papers, it is expected that some discussion of their subsequent impact should be present. The review should not exceed 1000 words.

Important Dates

The first session of the DTP Journal Club will be on 1st October 2014 in MPEB 1.19 from 2-4pm.

The deadline for the first individual paper review will be around middle of February 2015.

The deadline for the second individual paper review will be around June 2015.

Syllabus

Unless otherwise stated, the DTP Journal Club will be held on Wednesdays in MPEB 1.19 between 2-4pm.

First Rotation

1st October 2014: Welcome to the DTP Journal Club. 2-4pm in MPEB 1.19. Slides are available here.

8th October 2014: Presentation session.

1. 15th October 2014: Modeling dendrite density from magnetic resonance diffusion measurements. Jespersen SN et al. Neuroimage. 2007 Feb 15;34(4):1473-86. Lead by Gary Zhang. 

2. 22nd October 2014: Log-Euclidean Metrics for Fast and Simple Calculus on Diffusion Tensors Magnetic Resonance in Medicine V. Arsigny et al, 56:411–421 (2006). Lead by Tom Vercauteren.

3. 29th October 2014: Automatic classification of MR scans in Alzheimer’s disease, Stefan Kloppel et al. Brain (2008), 131, 681-689. Lead by Sebastien Ourselin. 3-4.30pm in MPEB 1.19.

4. 5th November 2014: Non-invasive mapping of connections between human thalamus and cortex using diffusion imaging, Behrens et al, Nature Neuroscience Vol 6 750-757 2003. Lead by Danny Alexander. See also Behrens 2003.

5. 12th November 2014: Session Postponed until January.

6. 19th November 2014: A Framework for the Volumetric Integration of Depth Images, Prisacariu, V.A. et al, ArXiv e-prints 1410.0925, 2014. Lead by Dan Stoyanov.

7. 26th November 2014: High-field MRI of brain cortical substructure based on signal phase. Jeff H. Duyn† et al, PNAS, 104, 28, 11796–11801, 2007. See also Liu et al 2014 for a review of SWI. Lead by Karin Shmueli.

8. 3rd December 2014: Magnetic resonance fingerprinting, Dan Ma et al, Nature 495, 187–192 (14 March 2013). Lead by David Atkinson.

9. 10th December 2014: Nonrigid registration using free-form deformations: application to breast MR images, D. Rueckert et al, IEEE Transactions on Medical Imaging 18:8, 712-721, 1999. Lead by Dave Hawkes. 2.30-4pm in MPEB 1.19.

14th January 2015: No session this week.

5. 21st January 2015: AxCaliber: a method for measuring axon diameter distribution from diffusion MRI. Assaf Y et al, Magn Reson Med. 2008 Jun;59(6):1347-54. Lead by Ivana Drobnjak.

28th January 2015: No session this week.

10. 4th February 2015: Stable Signal Recovery from Incomplete and Inaccurate Measurements. Candes E., Romberg J. and Tao T. Communications on Pure and Applied Mathematics, Vol. LIX, 1207–1223 (2006). Lead by Simon Arridge. See also the exercise provided here.

11. 11th February 2015: White, B.R. and Culver, J.P. (2010) Phase-encoded retinotopy as an evaluation of diffuse optical neuroimaging. NeuroImage 49, 568-577. Lead by Jem Hebden.

Second Rotation

12. 18th February 2015: Using the amide proton signals of intracellular proteins and peptides to detect pH effects in MRI. Jinyuan Zhou et al, Nature Medicine  9, 1085-1090 (2003). Lead by Xavier Golay

20th February 2015: First Written Review Due in.

13. 25th February 2015: Hoge RD et al. Linear coupling between cerebral blood flow and oxygen consumption in activated human cortex. Proc Natl Acad Sci U S A. 1999 Aug 3;96(16):9403-8. Lead by David Thomas.

14. 4th March 2015: [18F]T807, a novel tau positron emission tomography imaging agent, Chun-Fang Xia et al, Alzheimer's & Dementia. Volume 9, Issue 6, November 2013, Pages 666–676. Lead by Erik Arstad.

11th March 2015: No session this week.

15. 18th March 2015: Petibon Y et al. Towards coronary plaque imaging using simultaneous PET-MR: a simulation study. Phys Med Biol 2014; 59: 1203-22. See also Joshi et al 2014. Lead by Brian Hutton. To be held in Cruciform B404 - LT2.

16. 25th March 2015: Intra-arterial catheter for simultaneous microstructural and molecular imaging in vivo. Hongki Yoo et al VOLUME 17, NUMBER 12, DECEMBER 2011 nature medicine. Lead by Adrien Desjardins.

Term 3

17. 15th April 2015: Gleaning Multicomponent T1 and T2 Information From Steady-State Imaging Data. Sean C.L. Deoni et al. Magnetic Resonance in Medicine 60:1372–1387 (2008). Lead by Andrew Melbourne.

18. 17th April 2015: Ultrasonographically detectable markers of fetal chromosomal abnormalities. Nicolaides KH et al, Lancet, 340:8821, 704-707 1992. Lead by Anna David. Note that this is a Friday and will be held between 9-10.30am in MPEB 1.19!

19. 22nd April 2015: Whole-brain, time-locked activation with simple tasks revealed using massive averaging and model-free analysis. Javier Gonzalez-Castilloa, et al. PNAS, 2012, vol. 109, no. 14, 5487–5492. Lead by Louis Lemieux.

20. 29th April 2015: Lead by Paul Beard.

21. 6th May 2015: Lead by Matthew Clarkson.

22. 13th May 2015: Lead by Tammy Kalber.

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