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Journal Club

COURSE ORGANISERS:

Dr Andrew Melbourne, Dr Ivana Drobnjak

AIMS AND OBJECTIVES

Understanding and forming an accurate opinion of a journal article is a crucial skill for research; the CDT’s flagship journal club course 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.

Student Testimonials

I felt Journal Club helped my overall skills when facing academic/scientific papers and especially helped me organise scientific thought in a written way.

Student A


Journal club provided me with a very useful and comprehensive overview of a wide array of imaging research.

Student B
Assessment and Feedback

Students will be assessed through terms 1-3 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. Two example written reviews are available here and here.
Class Structure

In 2017/2018 the CDT 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 15 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 short 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 choose the paper in advance and will be there to help guide the discussion. Written reviews will be due in approximately half-way through the course and at the end of the student rotation.

The sessions are likely to last for at least 90 minutes with discussion.

Students will be divided into groups. One group will present the paper of that week, otherwise each group will be assigned one of the themes below:

  1. Aims & Motivation: What problem does this paper solve? Why has no one provided a solution before? Is sufficient background literature given to understand the problem?
  2. Experimental Design: Are the descriptions of the method, data and design sufficient to reasonably recreate the work?
  3. Supporting Results: Do the results follow from the methodology? are they sufficient? Are there superfluous results?
  4. Paper Limitations: Do the conclusions follow from the results or are they overstated? What limitations are present, do they undermine the results and conclusions?
  5. Paper Contributions: What does the paper add to the existing body of literature?
  6. Outcome & Impact: What impact has the paper made (citations, software, hardware, methods)? Is the paper likely to make a substantial impact in its field?

Current Syllabus - Important Dates 2017-18

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

First Rotation

4th October 2017: Welcome to the CDT Journal Club: Understanding Journal Publication

11th October 2017: Understanding Paper Structure and Paper Reading Exercise.

18th October 2017: Class structure and introductory presentations.

25th October 2017: Practice session with previous students.

Term 1

1st November 2017: Nuclear Induction, F. Bloch, Vol. 70 7/8, 1946. Led by Ivana Drobnjak. First official session.

8th November 2017: Go-ICP: A Globally Optimal Solution to 3D ICP Point-Set Registration. Yang et al, Pattern Analysis and Machine Intelligence, IEEE Transactions on . Led by Matt Clarkson.

15th November 2017: Unified segmentation. Ashburner J1, Friston KJ. Neuroimage. 2005 Jul 1;26(3):839-51. Led by Eugenio Iglesias.

22th November 2017: Automatic CT-ultrasound registration for diagnostic imaging and image-guided intervention. Wen W. et al. Medical Image Analysis, 12(5), 577-85. Led by Tom Vercauteren.

29th November 2017: Paper TBC. Led by Adrien Desjardins. This session will start at 1.30pm.

6th December 2017: An analytical model of restricted diffusion in bovine optic nerve. Stanisz et al. Magn. Reson. Med., 37: 103–111, 1997. Led by Gary Zhang.

13th December 2017: Real-Time Single Image and Video Super-Resolution Using an Efficient Sub-Pixel Convolutional Neural Network. Wenche Shi et al. 2016 CVPR/arXiv:1609.05158. Led by Christos Bergeles.

20th December 2017: No Session.

Term 2

10th January 2018: Paper TBC. Lead by Sebastien Ourselin.

Journal Club Syllabus 2016-17 (Archive)

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

First Rotation

5th October 2016: Welcome to the CDT Journal Club.

12th October 2016: Class structure and introductory presentations.

19th October 2016: Practice session with previous students.

26th October 2016: Active shape models—their training and application, Cootes et al, Computer Vision and Image Understanding archive. Volume 61 Issue 1, Jan. 1995, 38-59. Led by Eugenio Iglesias.

2nd November 2016: An analytical model of restricted diffusion in bovine optic nerve. Stanisz et al. Magn. Reson. Med., 37: 103–111, 1997. Led by Gary Zhang.

9th November 2016: Non-invasive mapping of connections between human thalamus and cortex using diffusion imaging. Behrens TE et al. Nat Neurosci. 2003 Jul;6(7):750-7. Led by Danny Alexander. To be held in 1.20 MPEB.

16th November 2016: Real-Time Single Image and Video Super-Resolution Using an Efficient Sub-Pixel Convolutional Neural Network. Wenche Shi et al. 2016 CVPR/arXiv:1609.05158. Led by Christos Bergeles.

23rd November 2016: Sergey M. Plis et al. Deep learning for neuroimaging: a validation study. Front. Neurosci., 20 August 2014 | http://dx.doi.org/10.3389/fnins.2014.00229. Led by Ivana Drobnjak.

30th November 2016: Automatic classification of MR scans in Alzheimer’s disease, Stefan Kloppel et al. Brain (2008), 131, 681-689. Led by Sebastien Ourselin.

7th December 2016: Session postponed.

14th December 2016: Multispectral Fluorescence Ultramicroscopy: Three-Dimensional Visualization and Automatic Quantification of Tumor Morphology, Drug Penetration, and Antiangiogenic Treatment Response. Michael Dobosz et al. Neoplasia Volume 16, Issue 1, January 2014. Led by Tammy Kalber.

21st December 2016: First Written Review Deadline.

Term 2

11th January 2017: Automatic CT-ultrasound registration for diagnostic imaging and image-guided intervention. Wen W. et al. Medical Image Analysis, 12(5), 577-85. Led by Tom Vercauteren.

18th January 2017: Functional near infrared spectroscopy (fNIRS) to assess cognitive function in infants in rural Africa. Lloyd-Fox S et al, Sci Rep. 2014 Apr 22;4:4740. Led by Clare Elwell. Starting at 1.30pm in MPEB 2.14.

25th January 2017: High contrast microstructural visualization of natural acellular matrices by means of phase-based x-ray tomography. Hagen, C.K. et al. Scientific Reports 5, Article number: 18156. For background see also Olivo and Castelli 2014. Led by Sandro Olivo.

1st February 2017: Session Postponed until March

8th February 2017: Phase-encoded retinotopy as an evaluation of diffuse optical neuroimaging. White BR, and Culver JP. Neuroimage. 2010 Jan 1;49(1):568-77. Led by Jem Hebden. Starting at 3pm

15th February 2017: No session this week.

22nd February 2017: 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. Led by David Thomas.

1st March 2017: Bayesian analysis of neuroimaging data in FSL. Woolwich et al, Neuroimage. 2009 Mar 31;45(1):S173-86. Led by John Ashburner.

8th March 2017: Magnetic resonance fingerprinting, Dan Ma et al, Nature 495, 187–192. Led by David Atkinson.

15th March 2017: Magnetic susceptibility mapping of brain tissue in vivo using MRI phase data. Shmueli K et al. Magn Reson Med. 2009 Dec;62(6):1510-22. Led by Karin Shmueli. To be held in Roberts 422.

26th April 2017: Neural Decoding of Visual Imagery During Sleep. T. Horikawa et al. Science 04 Apr 2013. Led by Adrien Desjardins

4th May 2017: Second Written Review Deadline 5pm.

May 2017: Final Feedback Session. Date TBC.

Journal Club Syllabus 2015-16 (Archive)
First Rotation

14th October 2015: Welcome to the CDT Journal Club.
21st October 2015: Presentation and Discussion Practice Session.
1. 28th October 2015: 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..
2. 4th November 2015: A positive-negative mode of population covariation links brain connectivity, demographics and behavior. Stephen M Smith et al. nature neuroscience advance online publication. Lead by Andre Altmann.
3. 11th November 2015: Automatic classification of MR scans in Alzheimer’s disease, Stefan Kloppel et al. Brain (2008), 131, 681-689. Lead by Sebastien Ourselin. Starting at 2.30pm.
4. 18th November 2015: Magnetic resonance fingerprinting, Dan Ma et al, Nature 495, 187–192 (14 March 2013). Lead by David Atkinson.
5. 25th November 2015: Functional near infrared spectroscopy (fNIRS) to assess cognitive function in infants in rural Africa. Lloyd-Fox S et al, Sci Rep. 2014 Apr 22;4:4740. Lead by Clare Elwell. Starting at 3pm.
6. 2nd December 2015: KinectFusion: Real-Time Dense Surface Mapping and Tracking, Richard A. Newcombe et al. IEEE ISMAR, 2011. Lead by Christos Bergeles. Starting at 3pm.
7. 9th December 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..
8. 16th December 2015: Gradient-based enhancement of tubular structures in medical images. Rodrigo Moreno and Örjan Smedby, Medical Image Analysis Volume 26, Issue 1, December 2015, Pages 19–29. Lead by Dean Barratt.
9. 13th January 2016: Modeling dendrite density from magnetic resonance diffusion measurements. Jespersen SN et al. Neuroimage. 2007 Feb 15;34(4):1473-86. Lead by Gary Zhang.
10. 20th January 2016: Automatic CT-ultrasound registration for diagnostic imaging and image-guided intervention. Wein, W., et al. (2008). Medical Image Analysis, 12(5), 577–85. Lead by Tom Vercauteren.
11. 27th January 2016: 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.

Second Rotation

12. 3rd February 2016: Brain-wide pathway for waste clearance captured by contrast-enhanced MRI. Jeffrey J. Iliff et al. The Journal of Clinical Investigation, Volume 123, Number, 2013 1299-1309. Lead by Mark Lythgoe.
13. 10th February 2016: MRI simulation-based evaluation of image-processing and classification methods, Kwan R.K. et al IEEE Transactions on Medical Imaging. 18(11):1085-97, Nov 1999. Lead by Ivana Drobnjak.
14. 17th February 2016: Real-time ultrasound transducer localization in fluoroscopy images by transfer learning from synthetic training data. Tobias Heimann et al, Medical Image Analysis, Volume 18, Issue 8, 2014, Pages 1320–1328. Lead by Dan Stoyanov.
15. 24th February 2016: Go-ICP: A Globally Optimal Solution to 3D ICP Point-Set Registration. Yang et al, Pattern Analysis and Machine Intelligence, IEEE Transactions on (Volume:PP Issue 99). Lead by Matt Clarkson.
16. 2nd March 2016: High-field MRI of brain cortical substructure based on signal phase.
Duyn JH et al, Proc Natl Acad Sci U S A. 2007 Jul 10;104(28):11796-801. See also Shmueli et al 2009. Lead by Karin Shmueli.
17. 9th March 2016: 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.
18. 16th March 2016: 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. To be held in the Front Engineering Building 1.03.
19. 23rd March 2016: Imaging brain deoxyglucose uptake and metabolism by glucoCEST MRI. Nasrallah F.A. et al. J Cereb Blood Flow Metab. 2013 Aug;33(8):1270-8. Lead by Xavier Golay.
20. 13th April 2016: 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.
22. 29th April 2016: Ultrasonographically detectable markers of fetal chromosomal abnormalities. Nicolaides KH et al, Lancet, 340:8821, 704-707 1992. Lead by Anna David. To be held on a Friday between 1-2.30pm.

JOURNAL CLUB SYLLABUS 2014-15 (ARCHIVE)

First Rotation
1st October 2014: Welcome to the DTP Journal Club.
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.

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.
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: Zhang HF, Maslov K, Stoica G, Wang L V. Functional photoacoustic microscopy for high-resolution and noninvasive in vivo imaging. Nat Biotechnol. 2006;24(7). See also Zhang 2007. Lead by Paul Beard.
21. 10th June 2015: Multiscale Imaging and Computational Modeling of Blood Flow in the Tumor Vasculature. Kim et al. Annals of Biomedical Engineering, Vol. 40, No. 11, November 2012 (Ó 2012) pp. 2425–2441. Lead by Rebecca Shipley.

22. 17th June 2015: Imaging adenoviral-directed reporter gene expression in living animals with positron emission tomography. Gambhir S et al, Proc. Natl. Acad. Sci. Vol. 96, pp. 2333–2338, March 1999. Lead by Tammy Kalber.
30th June 2015: Second Written Review due in.
23. 8th July 2015: Final Feedback Session.

DTP Syllabus 2009-2014 (Archive)

DTP Journal Club Syllabus 2013/2014

Rotation 1
1. 9th October 2013: Welcome to the DTP Journal Club.
2. 16th October 2013: No session this week.
3. 23rd October 2013: Modeling dendrite density from magnetic resonance diffusion measurements. Jespersen SN et al. Neuroimage. 2007 Feb 15;34(4):1473-86. Lead by Gary Zhang.
4. 30th October 2013: The clinical use of structural MRI in Alzheimer disease, Giovanni B. Frisoni et al, Nature Reviews Neurology 6, 67-77, February 2010. Lead by Sebastien Ourselin.
5. 6th November 2013: The Black Falcon: A Teleoperated Surgical Instrument for Minimally Invasive Surgery Akhil J. Madhani et al. Intl. Conference on Intelligent Robots and Systems 1998. Lead by Dan Stoyanov. To be held in Foster Court room 123.
7. 13th November 2013: [18F]T807, a novel tau positron emission tomography imaging agent for Alzheimer’s disease. Chun-Fang Xia, et al, Alzheimer’s & Dementia – (2013) 1–11. Lead by Erik Arstad. To be held in MPEB 1.19.
8. 20th November 2013: Magnetic resonance fingerprinting, Dan Ma et al, Nature 495, 187–192 (14 March 2013). Lead by David Atkinson.
9. 27th November 2013: Imaging brain deoxyglucose uptake and metabolism by glucoCEST MRI, Fatima A Nasrallah et al, Journal of Cerebral Blood Flow & Metabolism (2013), 1–9. Lead by Xavier Golay.
10. 4th December 2013: No session this week.
11. 11th December 2013: 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. To be held in MPEB 1.19.
12. 22nd January 2014: The importance of appropriate partial volume correction for PET quantification in Alzheimer’s disease. Thomas BA, et al. Eur J Nucl Med Mol Imaging 2011; 38: 1104-1119. See also the review paper. Lead by Brian Hutton. To be held in MPEB 1.19.
13. 5th February 2014 2pm: Deadline for the first written review.

Rotation 2
14. 5th February 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. To be held in MPEB 1.19.
15. 12th February 2014. First Feedback Session. To be held in MPEB 1.19.
16. 19th February 2014. Paper TBC. Chair TBC.
17. 26th February 2014. Visual assessment of the accuracy of retrospective registration of MR and CT images of the brain Fitzpatrick, J.M. et al. IEEE Transactions on Medical Imaging, 17, 4, 571-585, 1998. See also Gibson 2013. To be lead by Dean Barratt. To be held in Cruciform Foyer 101 Seminar Room 1.
18. 5th March 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 Haacke2005 for a review of iron imaging. Lead by Karin Shmueli. To be held in MPEB 1.19.
19. 12th March 2014. Magnetic resonance imaging of perfusion using spin inversion of arterial water. Williams DS et al, Proceedings of the National Academy of Sciences of the United States of America, 89(1), 212-216, 1992. Lead by David Thomas. To be held in MPEB 1.19.
20. 19th March 2014. 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. To be held in MPEB 6.12A.
21. 1st April 2014: Group Session Ultrasonographically detectable markers of fetal chromosomal abnormalities. Nicolaides KH et al, Lancet, 340:8821, 704-707 1992. Lead by Anna David. To be held in MPEB 1.19 2-3pm. Note that this is a Tuesday!
22. 4th April. Multiscale Imaging and Computational Modeling of Blood Flow in the Tumor Vasculature. Kim et al. Annals of Biomedical Engineering, Vol. 40, No. 11, November 2012 (Ó 2012) pp. 2425–2441. To be lead by Rebecca Shipley. To be held in MPEB 1.19. Note that this is a Friday!
23. 9th April 2014: No session this week.
24. 30th April 2014: 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. To be held in MPEB 1.19.
25. 23rd July 2014: Final Feedback Session. To be held in MPEB 2.14.

DTP Journal Club Syllabus 2012/2013

Term 1
1. 10th October 2012: Welcome to the DTP Journal Club.
2. 17th October 2012: 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.
3. 24th October 2012: Voxel-Based Morphometry – The Methods. John Ashburner and Karl J. Friston, NeuroImage, 11, 805-821 2000. Lead by Sebastien Ourselin.
4. 31th October 2012: No session this week.
5. 7th November 2012: No session due to PhD retreat.
6. 14th November 2012: An analytical model of restricted diffusion in bovine optic nerve, Greg J. Stanisz et al, Magnetic Resonance in Medicine, Volume 37, Issue 1, pages 103–111, January 1997. Lead by Gary Zhang.
7. 21st November 2012: Brain tissue sodium concentration in multiple sclerosis: a sodium imaging study at 3 tesla. Inglese M, et al. Brain. 2010 Mar;133(Pt 3):847-57. For background see Paling et al 2011. Lead by Claudia Wheeler-Kingshott
8. 28th November 2012: A System for Video-Based Navigation for Endoscopic Endonasal Skull Base Surgery. D. J. Mirota, et al. IEEE TRANSACTIONS ON MEDICAL IMAGING, VOL. 31, NO. 4, APRIL 2012. Lead by Dan Stoyanov.
9. 5th December 2012: No session this week.
10. 12th December 2012: In vivo imaging of glucose uptake and metabolism in tumors. S. Walker-Samuel et al, Nature Medicine, 2013, In Press. Lead by Xavier Golay.

Term 2
11. 16th January 2013: SENSE: Sensitivity encoding for fast MRI, KP Pruessmann et al. MAGNETIC RESONANCE IN MEDICINE 42:5 952-962 1999. Lead by David Atkinson.
12. 23rd January 2013: The importance of appropriate partial volume correction for PET quantification in Alzheimer’s disease. Thomas BA, et al. Eur J Nucl Med Mol Imaging 2011; 38: 1104-1119. See also the review paper. Lead by Brian Hutton.
13. 30th January 2013: Learning in the Fast Lane: New Insights into Neuroplasticity. Yaniv Sagi et al, Neuron, Volume 73, Issue 6, 1195-1203, 2012. Lead by Mark Lythgoe. To be held in MPEB 1.19.
14. 6th February 2013: No session this week.
15. 13th February 2013: Feedback Session.
16. 20th February 2013: High-field MRI of brain cortical substructure based on signal phase. Jeff H. Duyn† et al, PNAS, 104, 28, 11796–11801, 2007. See also Haacke2005 for a review of iron imaging. Lead by Karin Shmueli.
17. 27th February 2013: Automatic CT-ultrasound registration for diagnostic imaging and image-guided intervention. W. Wein et al. Medical Image Analysis,Volume 12, Issue 5, October 2008, Pages 577–585. Lead by Dean Barratt.
18. 6th March 2013: 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. To be held in MPEB 1.19.
19. 14th March 2013: Ultrasonographically detectable markers of fetal chromosomal abnormalities. Nicolaides KH et al, Lancet, 340:8821, 704-707 1992. Lead by Anna David. Note exceptionally this is on a Thursday and will be held in Anatomy B15.
20. 20th March 2013: 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.

Term 3
21. 10th April 2013: Magnetic resonance imaging of perfusion using spin inversion of arterial water. Williams DS et al, Proceedings of the National Academy of Sciences of the United States of America, 89(1), 212-216, 1992. Lead by David Thomas.
22. 17th April 2013: Finding Stationary Subspaces in Multivariate Time Series. Paul von Bünau et al. Phys. Rev. Lett. 103, 214101 (2009). See also von Bünau 2010 and a review paper Naci 2012. Lead by Louis Lemieux.
23. 24th April 2013: White, B.R. and Culver, J.P. (2010) Phase-encoded retinotopy as an evaluation of diffuse optical neuroimaging. NeuroImage 49, 568-577. See also the adjacent supplementary material. Lead by Jem Hebden. To be held in Roberts 105b.
24. 22nd May 2013: Final Feedback Session. To be held in MPEB 2.14.

DTP Journal Club Syllabus 2011/2012

Term 1
1. 5th October 2011: Welcome to the DTP Journal Club.
2. 12th October 2011: 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.
3. 19th October 2011: Voxel-Based Morphometry – The Methods. John Ashburner and Karl J. Friston, NeuroImage, 11, 805-821 2000. Lead by Sebastien Ourselin.
4. 26th October 2011: Imaging Brain Amyloid in Alzheimer’s Disease with Pittsburgh Compound-B. Klunk et al, Ann Neurol, 55, 306–319 2004. Lead by Erik Arstad.
5. 2nd November 2011: SENSE: Sensitivity encoding for fast MRI, KP Pruessmann et al. MAGNETIC RESONANCE IN MEDICINE 42:5 952-962 1999. Lead by David Atkinson. To be held in MPEB 1.19.
6. 9th November 2011: Dysmyelination revealed through MRI as increased radial (but unchanged axial) diffusion of water. Song SK et al. Neuroimage. Nov;17(3):1429-36. 2002. See also Sun et al. Lead by Claudia Wheeler-Kingshott.
7. 16th November 2011: Ultrasonographically detectable markers of fetal chromosomal abnormalities. Nicolaides KH et al, Lancet, 340:8821, 704-707 1992. Lead by Anna David.
8. 23rd November 2011: 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.
9. 30th November 2011: Evoked brain responses are generated by feedback loops. Garrido et al, Proc Natl Acad Sci USA. 104(52):20961-6, 2007 . Lead by Will Penny.
10. 7th December 2011: Brain magnetic resonance imaging with contrast dependent on blood oxygenation. Ogawa S et al, Proceedings of the National Academy of Sciences of the United States of America, 87(24), 9868-9872, 1990. Lead by Xavier Golay. To be held in MPEB 1.19.
11. 14th December 2011: Magnetic resonance imaging of perfusion using spin inversion of arterial water. Williams DS et al, Proceedings of the National Academy of Sciences of the United States of America, 89(1), 212-216, 1992. Lead by David Thomas. To be held from 12-1pm in MPEB 2.14.

Term 2
12. 11th January 2012: Multicolor and electron microscopic imaging of connexin trafficking. Gaietta G, et al. Science, 296(5567), 503-507, 2002. Lead by David Becker.
13. 18th January 2012: No session.
14. 25th January 2012: Multimodality imaging of structure and function, D Townsend, Phys. Med. Biol., 53, 2008 R1–R39. Lead by Brian Hutton.
15. 1st February 2012: Deadline for first written review.
16. 8th February 2012: An analytical model of restricted diffusion in bovine optic nerve, Greg J. Stanisz et al, Magnetic Resonance in Medicine, Volume 37, Issue 1, pages 103–111, January 1997. Lead by Gary Zhang.
17. 15th February 2012: Maze training in mice induces MRI-detectable brain shape changes specific to the type of learning NeuroImage 54 (2011) 2086–2095. Lead by Mark Lythgoe. To be followed by first feedback session.
18. 22nd February 2012: No session.
19. 29th February 2012: No session.
20. 7th March 2012: Functional photoacoustic microscopy for high-resolution and noninvasive in vivo imaging. Zhang et al, Nature Biotechnology, 2006. 24(7): p. 848-851. See also Zhang 2007. Lead by Paul Beard. To be held in MPEB 1.19.
21. 14th March 2012: Three-dimensional multi-scale line filter for segmentation and visualization of curvilinear structures in medical images. Sato et al. Medical Image Analysis, Volume 2, Issue 2, June 1998, Pages 143-168. Lead by Dean Barratt. To be held in Rockefeller 339.
22. 21st March 2012: White, B.R. and Culver, J.P. (2010) Phase-encoded retinotopy as an evaluation of diffuse optical neuroimaging. NeuroImage 49, 568-577. See also the adjacent supplementary material. Lead by Jem Hebden.
23. 28th March 2012: Dynamic magnetic resonance imaging of human brain activity during primary sensory stimulation. Kwong KK et al, Proc Natl Acad Sci USA. 15;89(12):5675-9, 1992. Lead by Nikolaus Weiskopf.

Term 3
24. 18th April 2012: Electrophysiological correlates of the brain’s intrinsic large-scale functional architecture, Biyu J. He et al, 2008, PNAS, vol.105, no.41,16039–16044. Lead by Louis Lemieux.
25. 25th April 2012: No session.
26. 2nd May 2012: 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. Lead by Simon Arridge. See also the exercise provided here.
27. 9th May 2012: No session due to ISMRM conference.
28. 16th May 2012: Ventral and dorsal pathways for language. Saur D et al. PNAS, Nov 2008, vol 105, 46, 18035-18040. Lead by Torsten Baldeweg.
29. 18th May 2012: Prostate Cancer Foci Detected on Multiparametric Magnetic Resonance Imaging are Histologically Distinct From Those Not Detected. Andrew B. Rosenkrantz et al. The Journal of Urology, 2032-2038, 2012. Lead by Shonit Punwani. Note that this is on Friday at 11am and will be held in MPEB 1.19.
30. 23rd May 2012: High-field MRI of brain cortical substructure based on signal phase. Jeff H. Duyn† et al, PNAS, 104, 28, 11796–11801, 2007. See also Haacke2005 for a review of iron imaging. Lead by Karin Shmueli. *31. 6th June 2012: Provisional deadline for second written review, 5pm.
32. 20th June 2012: Final feedback session.

DTP Journal Club Syllabus 2010/2011

Term 1 *1. 6th October 2010: Welcome to the DTP Journal Club.
2. 13th October 2010: The clinical use of structural MRI in Alzheimer disease, Giovanni B. Frisoni et al, Nature Reviews Neurology 6, 67-77, February 2010. Lead by Xavier Golay.
3. 20th October 2010: Diffusion-weighted MR imaging of anisotropic water diffusion in cat central nervous system. Moseley ME et al, Radiology, 176(2), 439-445, 1990. Lead by David Atkinson.
4. 27th October 2010: Imaging Brain Amyloid in Alzheimer’s Disease with Pittsburgh Compound-B. Klunk et al, Ann Neurol, 55, 306–319 2004. Lead by Erik Arstad.
5. 3rd November 2010: Multicolor and electron microscopic imaging of connexin trafficking. Gaietta G, et al. Science, 296(5567), 503-507, 2002. Lead by David Becker. To be held in MPEB 1.04.
6. 10th November 2010: Active Shape Models-Their Training and Application, Cootes T. F. et al, Computer Vision and Image Understanding, 61:1, 38-59, 1995. Lead by Sebastien Ourselin.
7. 17th November 2010: Multimodality imaging of structure and function, D Townsend, Phys. Med. Biol., 53, 2008 R1–R39. Lead by Brian Hutton.
8. 24th November 2010: 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. To be held in MPEB 1.19.
9. 15th December 2010: 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. To be held in MPEB 2.14.

Term 2
10. 12th January 2011: Dynamic contrast enhanced, pelvic phased array magnetic resonance imaging of localized prostate cancer for predicting tumor volume: correlation with radical prostatectomy findings. Villers A et al, J Urol. 176(6 Pt 1), 2432-7, 2006. Lead by Shonit Punwani.
11. 19th January 2011: Dynamic magnetic resonance imaging of human brain activity during primary sensory stimulation. Kwong KK et al, Proc Natl Acad Sci USA. 15;89(12):5675-9, 1992. Lead by Nikolaus Weiskopf.
12. 2nd February 2011: First written review due in see brief.
13. 9th February 2011: Feedback Session.
1. 16th February 2011: Global and local fMRI signals driven by neurons defined optogenetically by type and wiring. Lee et al, Nature, 2010, 465(7299), pp788-792. Lead by Mark Lythgoe. To be held from 2.30pm in MPEB 2.14.
2. 23rd February 2011: Evoked brain responses are generated by feedback loops. Garrido et al, Proc Natl Acad Sci USA. 104(52):20961-6, 2007. Lead by Will Penny.
3. 2nd March 2011: Dysmyelination revealed through MRI as increased radial (but unchanged axial) diffusion of water. Song SK et al. Neuroimage. Nov;17(3):1429-36. 2002. See also Sun et al. Lead by Claudia Wheeler-Kingshott. To be held in MPEB 1.19.
4. 9th March 2011: Snapshot Imaging at 0.5 Tesla using Echo-Planar Techniques, Ordidge RJ et al. Magn Reson Med 10:227-240, 1989. Lead by Roger Ordidge.
5. 16th March 2011: Magnetic resonance imaging of perfusion using spin inversion of arterial water. Williams DS et al, Proceedings of the National Academy of Sciences of the United States of America, 89(1), 212-216, 1992. Lead by David Thomas. To be held in MPEB 1.19.
6. 23rd March 2011: Three-dimensional multi-scale line filter for segmentation and visualization of curvilinear structures in medical images. Sato et al. Medical Image Analysis, Volume 2, Issue 2, June 1998, Pages 143-168. Lead by Dean Barratt.
7. 30th March 2011: Ultrasonographically detectable markers of fetal chromosomal abnormalities. Nicolaides KH et al, Lancet, 340:8821, 704-707 1992. Lead by Anna David.
8. 6th April 2011: Negative functional MRI response correlates with decreases in neuronal activity in monkey visual area V1. Shmuel A. et al, Nature Neuroscience 9, 569-577, 2006. See also Logothetis 2001. Lead by Louis Lemieux. To be held in MPEB 1.19.
9. 13th April 2011: Functional photoacoustic microscopy for high-resolution and noninvasive in vivo imaging. Zhang et al, Nature Biotechnology, 2006. 24(7): p. 848-851. See also Zhang 2007. Lead by Paul Beard.

Term 3
10. 4th May 2011: Inverse Problems with Structural Prior Information, J. P. Kaipio et al, Inverse Problems, 15, 713-729, 1999. Lead by Simon Arridge. To be held in MPEB 1.19.
11. 18th May 2011: Second written review due in.
12. 25 May 2011: Feedback session.

DTP Journal Club Syllabus 2009/2010

Term 1
1. 7th October 2009: Welcome to the DTP Journal Club
2. 14th October 2009: 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 MRM 2003.
3. 21st October 2009: Active Shape Models-Their Training and Application, Cootes T. F. et al, Computer Vision and Image Understanding, 61:1, 38-59, 1995. Lead by Sebastien Ourselin. To be held in MPEB 2.14 1-2pm.
4. 28th October 2009: Multimodality imaging of structure and function, D Townsend, Phys. Med. Biol., 53, 2008 R1–R39. Lead by Brian Hutton.
5. 4th November 2009: MK-9470, a positron emission tomography (PET) tracer for in vivo human PET brain imaging of the cannabinoid-1 receptor, H. Donald Burns et al, PNAS, 104:23: 9800–9805, 2007. Lead by Erik Arstad.
6. 11th November 2009: SENSE: Sensitivity encoding for fast MRI, KP Pruessmann et al. MAGNETIC RESONANCE IN MEDICINE 42:5 952-962 1999. Lead by David Atkinson.
7. 18th November 2009: Inverse Problems with Structural Prior Information, J. P. Kaipio et al, Inverse Problems, 15, 713-729, 1999. Lead by Simon Arridge.
8. 25th November 2009: 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. See also Arun IEEE-PAMI 1987. Lead by Dave Hawkes.
9. 2nd December 2009: Snapshot Imaging at 0.5 Tesla using Echo-Planar Techniques, Ordidge RJ et al. Magn Reson Med 10:227-240, 1989. Lead by Roger Ordidge.
10. 9th December 2009: Evoked brain responses are generated by feedback loops. Garrido et al, Proc Natl Acad Sci USA. 104(52):20961-6, 2007. Lead by Will Penny.
11. 18th December 2009 (Friday): First Term Feedback Session

Term 2
1. 20th January 2010: Multicolor and electron microscopic imaging of connexin trafficking. Gaietta G, et al. Science, 296(5567), 503-507, 2002. Lead by David Becker.
2. 27th January 2010: Diffusion-weighted MR imaging of anisotropic water diffusion in cat central nervous system. Moseley ME et al, Radiology, 176(2), 439-445, 1990. Lead by Matt Hall.
3. 3rd February 2010: Brain magnetic resonance imaging with contrast dependent on blood oxygenation. Ogawa S et al, Proceedings of the National Academy of Sciences of the United States of America, 87(24), 9868-9872, 1990. Lead by Xavier Golay.
4. 10th February 2010: Session postponed until third term.
5. 17th February 2010: Multishot diffusion-weighted fast spin-echo using PROPELLER MR. James G Pipe et al, Magn Reson Med, 47:1, 42-52, 2002. Lead by David Atkinson.
6. 24th February 2010: Multimodality Image Registration by Maximization of Mutual Information. F. Maes et al, IEEE TRANSACTIONS ON MEDICAL IMAGING, 16:2, 187-198, 1997. See also Viola 1995 and Studholme 1999. Lead by Dave Hawkes.
7. 3rd March 2010: Ultrasonographically detectable markers of fetal chromosomal abnormalities. Nicolaides KH et al, Lancet, 340:8821, 704-707 1992. See also Donald 1958. Lead by Anna David. To be held in MPEB 2.14.
8. 10th March 2010: Magnetic resonance imaging of perfusion using spin inversion of arterial water. Williams DS et al, Proceedings of the National Academy of Sciences of the United States of America, 89(1), 212-216, 1992. Lead by David Thomas.

Term 3
1. 28th April 2010: Dynamic contrast enhanced, pelvic phased array magnetic resonance imaging of localized prostate cancer for predicting tumor volume: correlation with radical prostatectomy findings. Villers A et al, J Urol. 176(6 Pt 1), 2432-7, 2006. Lead by Shonit Punwani.
2. 5th May 2010: Zhang, HF, Maslov, K, Stoica, G, and Wang, LV, Functional photoacoustic microscopy for high-resolution and noninvasive in vivo imaging. Nature Biotechnology, 2006. 24(7): p. 848-851. See also Zhang 2007. Lead by Paul Beard.
3. 12th May 2010: In vivo visualization of gene expression using magnetic resonance imaging. Louie AY et al, Nature biotechnology, 18(3), 321-325, 2002. Lead by Mark Lythgoe.
4. 19th May 2010: Automated model-based tissue classification of MR images of the brain. Van Leemput et al, IEEE TMI, 18:10,897-908, 1999. Lead by Sebastien Ourselin.
5. 14th June 2010 (Monday): Final Feedback Session