Not Another Ranking...

This week, I found out about a new ranking: ScimagoIR. There are rankings for schools, universities, but this ranking is for research institutions, either hospitals, companies, universities or public institutes. I am not a great advocate for rankings, but at the same time it is always interesting to look at this data. Furthermore, the ranking can be seen by country and several parameters are showed: number of publications, percentage of publication with international collaborators, percentage of publications in top journals, scientific leadership, ... I found out that my institution is actually one of the leaders of the ranking!

ERC Starting Grant Winners

ERC awards the most important grants to researchers in Europe. For young researchers (2-7 years after PhD), the ERC has Starting Grants. The goal for these starting grants is for these young researchers to start their own group and line of research. This year results have been published (here) and of course, I checked which of these grants are related to medical imaging. There were 3329 applications and 287 researchers were successful. The ERC grants are divided in three big areas: 1) Physical Sciences and Engineering, 2) Life Sciences, 3) Social Sciences and Humanities. Medical imaging fits in Life Sciences and more concretely in LS7 - Diagnostic tools. There were 8 starting grants related to Medical Imaging:

Daniela Thorwarth, Erlangen University, Germany - Biologically individualized, model-based  radiotherapy on the basis of multi-parametric molecular tumour profiling.

Julien Valette, CEA, France - Exploring brain intracellular space using diffusion-weighted NMR spectroscopy in vivo

Galia Blum, The Hebrew University of Jerusalem, Israel - Protease Activated X-Ray Contrast Agents for 

Molecular Imaging of Vulnerable Atherosclerotic Plaques and Cancer Development using Spectral CT.

Rachel Katz-Brull, Hadassah Medical Organization, Israel - Citicoline and deoxyglucose as new molecular imaging probes of DNP hyperpolarized MRI for cancer and neuroimaging

Niv Papo, Ben-Gurion University of the Negev, Israel - Developing Multispecific Biological Agents that
Target Tumor Neovasculature for Cancer Imaging and Therapy

Francesco Ricci, University of Rome "Tor Vergata", Italy - Nature-inspired theranostic nanodevices for tumor imaging, early diagnosis and targeted drug-release

Mangala Srinivas, Radboud University Nijmegen, The Netherlands - Clinical ultrasound platform for the quantitative and longitudinal imaging of theranostics and cellular therapy

Jaco Zwanenburg, University Medical Centre, Utrecht, The Netherlands - Towards understanding cerebral small vessel disease: Innovative, MRI-based, functional markers to discover the terra incognita between large vessels and macroscopic brain lesions

Congratulations to all the winners! But I still have a favorite grant and therefore, one of the papers related to that grant can be read here:

Daniela Thorwarth, Susanne-Martina Eschmann, Frank Paulsen, Markus Alber. (2006). Hypoxia Dose Painting by Numbers: A Planning Study International Journal of Radiation Oncology * Biology * Physics DOI: 10.1016/j.ijrobp.2006.11.061

Statistics - Love or Hate?

There is no clinical medical imaging paper without statistics. Research can't live without it, but most researchers wish they could. Big Picture is a Welcome Trust magazine, which is directed to teachers and students. Therefore, the magazine has really simple and clear examples. The new issue is about statistics. There is lots of information relevant for medical imaging researchers: 1) the story about the advertisement of a CT scan that was forbidden to broadcast, 2) types of medical studies from the statistic point of view (see picture below) and 3) general concepts about research. See more information here.

The new issue pdf can be read here. The previous issue was about medical neuroimaging, which can be read here.

Europe PubMed Central

Yesterday, I have discovered the Europe PubMed Central webpage. This is the European version of the PubMed Central. You can find articles and abstracts, but that you already can find online with Google Scholar. What interested me in this webpage is that you find out more about projects and grants funded in Europe in the tool Grant Lookup. In a time of crisis, not only we want to know how our money is being spent, but also find places where our research might be also important in a time where researchers are the new nomads...

Procrastination to find the most cited paper in the field of MRI

I have posted recently about the most cited (important?) papers in Medical Imaging in the last ten/five/two years here. Today I look for the most cited papers in the field of MRI. Interesting to note that these 3 papers were published in Neuroimage.

Most cited paper in Radiology, Nuclear Science and Medical Imaging Field about MRI:

- of the last 10 years with 1346 citations:
Ashburner, J., & Friston, K. (2005). Unified segmentation NeuroImage, 26 (3), 839-851 DOI: 10.1016/j.neuroimage.2005.02.018 

This paper is the basis for the SPM framework, one of the most important in the field of MRI. Thus, it is understandable that this paper has a lot of citations, because most researchers who use this framework (and there are a lot, myself included) use this paper in their citations.

- of the last 5 years with 250 citations:
Klein, A., Andersson, J., Ardekani, B., Ashburner, J., Avants, B., Chiang, M., Christensen, G., Collins, D., Gee, J., Hellier, P., Song, J., Jenkinson, M., Lepage, C., Rueckert, D., Thompson, P., Vercauteren, T., Woods, R., Mann, J., & Parsey, R. (2009). Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration NeuroImage, 46 (3), 786-802 DOI: 10.1016/j.neuroimage.2008.12.037

I have to say that I am quite surprised by finding this paper on top. Brain MRI registration is nowadays considered almost a solved problem and I don't think there are many people looking into this anymore. However, it is always nice to put in your own paper: "I used this registration, because this paper says it is the best".

- of the last 2 years with 106 citations:
Smith, S., Miller, K., Salimi-Khorshidi, G., Webster, M., Beckmann, C., Nichols, T., Ramsey, J., & Woolrich, M. (2011). Network modelling methods for FMRI NeuroImage, 54 (2), 875-891 DOI: 10.1016/j.neuroimage.2010.08.063

I have talked about brain networks some times in this blog and this paper shows me that this topic has been hot in the last two years. This papers discusses different methods to obtain networks with fMRI data: "Many different methods are being used in the literature, but almost none has been carefully validated or compared for use on FMRI timeseries data."

European Month of the Brain

Today starts the European Month of the Brain. I certainly hoped that this information would have been publicized much more. I only come to this information by chance. Let's hope we hear more about this during this month!

"Brain research in Europe needs a decisive effort. We must invest more, define clearer and more innovative research and healthcare strategies, and better coordinate national efforts. We therefore decided to make May 2013 the European Month of the Brain - a full month packed with events and activities to make decision-makers, stakeholders, the media and the public aware of the successes achieved and the challenges still laying ahead for brain research."



The main webpage is here and links about funding are also very useful.

Procrastination to find the most cited papers in Medical Imaging

Few day ago, I was wondering what were the most cited (important?) papers in Medical Imaging in the last ten/five/two years. The problem was that I didn't know exactly how to find this information. I googled a bit around and I found a way and tried it out. I found also some extra information about the subject:

Published Papers in Radiology, Nuclear Science and Medical Imaging Field:

Citations in Radiology, Nuclear Science and Medical Imaging Field:

It is interesting to note that it is increasing steadily every year. 

Most cited paper in Radiology, Nuclear Science and Medical Imaging Field:

- of the last 10 years
Jan, S., Santin, G., Strul, D., Staelens, S., Assié, K., Autret, D., Avner, S., Barbier, R., Bardiès, M., Bloomfield, P., Brasse, D., Breton, V., Bruyndonckx, P., Buvat, I., Chatziioannou, A., Choi, Y., Chung, Y., Comtat, C., Donnarieix, D., Ferrer, L., Glick, S., Groiselle, C., Guez, D., Honore, P., Kerhoas-Cavata, S., Kirov, A., Kohli, V., Koole, M., Krieguer, M., Laan, D., Lamare, F., Largeron, G., Lartizien, C., Lazaro, D., Maas, M., Maigne, L., Mayet, F., Melot, F., Merheb, C., Pennacchio, E., Perez, J., Pietrzyk, U., Rannou, F., Rey, M., Schaart, D., Schmidtlein, C., Simon, L., Song, T., Vieira, J., Visvikis, D., Walle, R., Wieërs, E., & Morel, C. (2004). GATE: a simulation toolkit for PET and SPECT Physics in Medicine and Biology, 49 (19), 4543-4561 DOI: 10.1088/0031-9155/49/19/007
- of the last 5 years
Klein, S., Staring, M., Murphy, K., Viergever, M., & Pluim, J. (2010). elastix: A Toolbox for Intensity-Based Medical Image Registration IEEE Transactions on Medical Imaging, 29 (1), 196-205 DOI: 10.1109/TMI.2009.2035616

- of the last 2 years
Hricak, H., Brenner, D., Adelstein, S., Frush, D., Hall, E., Howell, R., McCollough, C., Mettler, F., Pearce, M., Suleiman, O., Thrall, J., & Wagner, L. (2010). Managing Radiation Use in Medical Imaging: A Multifaceted Challenge Radiology, 258 (3), 889-905 DOI: 10.1148/radiol.10101157
How to find this information?
Go to Web of Knowledge and follow these tutorial:
http://www.umuc.edu/library/libhow/woshighlycited_tutorial.cfm

The best blogs in Neuroscience

With the new community of Research Blogging, I have come across with 4 blogs, which are probably the most famous and known in the neuroscience blogosphere of research blogging:



Image from here.

The Scicurious Brain: the Good, Bad, and  Weird in Psychology and Neuroscience and my recommended articles are:
- Beer, Dopamine and Brain Scans
- The BRAIN initiative: BAM or BUST?

Neuroskeptic and my recommended articles are:
- The Man with Uncrossed Eyes
- What is wrong with "Publish or Perish"?

Neurocritic and my recommended articles are:
-  How Neuroscientists Scan the Media
- What Is This Thing Called Neuroscience?

Brain Posts and my recommendation articles are:
- DTI identifies Brain Aging Changes
- Blast-related Traumatic Brain Injury

These blogs are from this moment in the blog list on the right side of this blog. Did you already know these blogs? Or know other very good ones?

Research Blogging

This blog is now part of the community in researchblogging.org. "ResearchBlogging.org is a system for identifying the best, most thoughtful blog posts about peer-reviewed research." Know Your Images is now one of the blogs which ResearchBlogging checks for posts about peer-reviewed articles. Furthermore, it is a great way to find new blogs and also keeps you updated about the blogs you like.

Of course, this blog will keep a fare amount of posts which are not dedicated to peer-reviewed articles, but which are just fun to know about and watch.

NFL (National Football League) and medical imaging

I have recently talked about the brain injuries in Superbowl players here and there are updated news about this. NFL (National Football League) is supporting a deeper study about these injuries and also how to prevent them. Some are afraid that this will kill the practice of football, but I think it is important that NFL starts taking these health issues seriously. Eventually, this research can even result in broader scientific knowledge.


Image from here.

Links:
http://www.reuters.com/article/2013/03/11/us-nfl-concussion-idUSBRE92A0UT20130311
http://edition.cnn.com/2013/01/29/health/nfl-harvard-study
http://www.newyorker.com/online/blogs/elements/2013/04/how-damaged-are-nfl-players-brains.html

TEDMED 2013

I hope you have already heard about TED before (if not, seriously check it out here). TEDMED is a TED conference dedicated only to medical issues and it starts today. I hope medical imaging will be part of some talks...

The schedule of the conference is here, but most important it is possible to watch the conference online in real-time or on-demand following a couple of instructions. I'll see it later on-demand according to my interests and time. Right now, the talks I am looking forward are:
- Can Science take the next leap? by Francis Collins
- What's the 21st century version of prevention? by Danny Hillis
- How can we improve health care if doctors don't know if they do any good? by Michael E. Porter

The TEDMED experience:

The videos from last year can be accessed online in TEDMED youtube channel.

Procrastination with Scientific Social Networks

I have written before about Google Scholar as a way to follow your co-authors, colleagues or just to get alerts from a certain topic. Today, I talk about other websites that have nice features which Google Scholar doesn't have and which can be useful: BiomedExperts, ResearchGate and Academia.edu.

 


BiomedExperts is a scientific social network for biomedical experts.The main features of this webpage are the visualization tools about researchers. You can see the published topics, published articles, co-authors, times and places, network view and geonetwork view. These two last ones are very nice to visualize and give you information that Google Scholar doesn't provide you.

ResearchGate is another scientific network, but it is available for all research topics. It has basically all the features of BiomedExperts, expect the network visualization, but it has other ones, such as citation management, endorsement management (like LinkedIn) and even allows you to publish data (or download it).





Academia.edu is another scientific network with a lot of users. The main difference from the other two is that it allows you to put papers which are not finished or were not accepted. The thing I most like in this webpage is that it gives me an alert whenever my profile appears in google results, so basically I know when other researchers googled me and which words they used for that.

This post was an idea from a fellow researcher.

Obama's BRAIN Initiative

On the 2nd April, President Obama has made a speech about a new initiative to study the brain. This new initiative is called BRAIN - Brain Research through Advancing Innovative Neurotechnologies.This initiative has been inspired in the Genome Project. His speech can be seen here or read here.



For me, the most important remark was: "So there is this enormous mystery waiting to be unlocked, and the BRAIN Initiative will change that by giving scientists the tools they need to get a dynamic picture of the brain in action and better understand how we think and how we learn and how we remember. " My work is close to this idea using, of course, medical imaging, so I am really interested in this initiative.




About the budget involved, it might be considerably smaller than the Genome Project (3.8 billion), but the announced kick-start for the project was about 100$ million, while for the Genome Project was 28$ million. This kick-start will fund projects in the scope of the initiative: 50$ million from DARPA, 40$ million from NIH and 20$ million from NSF. Private sector will also contribute about 158$ million: 60$ million from the Allen Institute for Brain Science, 30$ million from the Howard Hughes Medical Institute, 28$ million from Salk Institute for Biological Studies and 4$ million from the Kavli Foundation, among others.

White House links: Blog, Fact Sheet and Infographics

PhD: to do or not to do?

Following yesterday's post about post-docs, today I talk about PhDs. Most people finish their Master and want to land their first job, other think there is more than finding a job and feel that they have to learn more. These ones end up doing a PhD. If you should do or not, depends on the professional career you want to have. I have not regret at any moment to do a PhD, but maybe that is just me:

http://news.ycombinator.com/item?id=180743

http://www.urch.com/forums/phd-economics/130858-top-5-reasons-do-not-do-phd.html

http://www.findaphd.com/student/study/study-16.asp

http://www.guardian.co.uk/higher-education-network/blog/2012/may/03/phd-doctorate-higher-education-love-money

Do you think a PhD is a must or a over-qualification for your career?

Post-doc: industrial or academic?

After doing a PhD, it is time to start thinking what to do next. You can leave research, but if you decide that research is what you want to do, a post-doc is the natural path. You have to think about doing an industrial or an academic post-doc. Both options have advantages and disadvantages and one has to take into account that Europeans and Americans have different views.

I found some interesting articles about this topic, which can be read here:
http://www.nature.com/naturejobs/science/articles/10.1038/nj6989-324a
http://chronicle.com/forums/index.php/board,28.0.html
http://blog.1degreebio.org/?bid=54
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2008_06_13/science.opms.r0800055
http://scienceadvocacy.org/Blog/2011/01/06/academia-vs-industry-a-former-postdoc%E2%80%99s-perspective/

What do you think? Do you know people which have taken different paths?

Gorillla CT scan

Can you find the Gorilla in this image?



I took at least 10 seconds to spot it. This image was used in a study with radiologists, where they were asked if there is something wrong with the image. 83% of radiologist didn't see the gorilla. This doesn't mean that the radiologist don't pay attention to the images, but rather that they will not see what they aren't looking for... Please see the video that inspired this study in the links and understand better what this means.

Links:
http://www.theinvisiblegorilla.com/videos.html
http://life.nationalpost.com/2013/02/13/dancing-gorilla-image-on-ct-scan-passed-over-by-more-than-80-of-radiologists-study-finds/

Databases of Medical Images

Medical Image Databases are great to work on medical imaging processing and sometimes to get a feeling of the images before using real data. I have found some databases in the internet that I consider quite interesting:


Minimal Interval Resonance Imaging in Alzheimer's Disease MIRIAD
This database is focused on Alzheimer Diseases patients, but also control patients.

Mini Mammographic Image Analysis Society Database Mini-MIAS
A database with mammograms and with medical information.

Medpix Teaching database MedPix
A database with examples to teach from CT to MRI.

Retrospective Image registration Evaluation RIRE
A database with images to register and the ground truth to compare.

Alzheimer's Disease Neuroimaging Initiative ADNI
This a huge database of patients images with PET and MRI.

Do you know other good databases?

The Human Brain Project

The European Commission has officially announced the selection of the Human Brain Project (HBP) as one of its two FET (Future and Emerging Technologies) Flagship projects. The new project will coordinate European efforts to address one of the greatest challenges of modern science: understanding the human brain.

"Understanding the human brain is one of the greatest challenges facing 21st century science. If we can rise to the challenge, we can gain profound insights into what makes us human, develop new treatments for brain diseases and build revolutionary new computing technologies."


"According to a recent report, nearly one-third of the European population is affected by some kind of psychiatric or neurological disease (anxiety, mood disorders, neurodegenerative disease, etc.)."

The promoting video is very instructive and I'm very exciting about the database with medical images, of course... I hope this project will be very successful!

Open-source journals

Among researchers, there has been great discussion about journals and their subscriptions. The main argument is that journals are making money easily: researchers write the articles and other researchers review them for free, while universities and institutes are paying expensive subscriptions fees to access those articles. Therefore, many researchers are turning their papers to open-source journals. In this case, the access to the articles is free, while researchers pay to publish their articles. As a open-source fan, I was always thinking how great it is that things are changing, until I read an opinion article from Simon Cherry. Simon Cherry is the new Editor-in-Chief of the journal, “Physics in Medicine and Biology”. The journal is one of the top-ranked biomedical engineering journals.I have talked with Simon Cherry about my work in conferences and I greatly admire him. Just last year, in Anaheim NSS/MIC conference, he was awarded "The Edward J. Hoffman Medical Imaging Scientist Award"and his speech was just great to hear!

Simon Cherry's article "Open Access and PMB"
Short article about his new role:
http://www.bme.ucdavis.edu/articles/2011/10/06/simon-cherry-editor-physics-medicine-biology/Si
Simon Cherry's Lab:
http://www.bme.ucdavis.edu/cherrylab/

Invest in Science

 There has been some discussion in Europe about funding science. Europe has always invested less money and less strategically in Science than USA, and we are losing our best brains... Gottfried Schatz, a prize winning biologist, which has worked in Europe and USA, has called European funding MESS: Mediocre European Science System. Although I think he is being too radical about the science system, he might prove to be correct in the future if investment in science stops. A petition with more than 150.000 signatures in being held in: http://www.no-cuts-on-research.eu/.

Recently, I came across this webpage http://investinscience.eu/category/videos/ , where researchers and other can post videos to promote science in Europe. Without much effort, they are better than the infamous videos that the European Comission made:

Links:
European Science Foundation - http://www.esf.org/
European Commission CORDIS - http://cordis.europa.eu/home_en.html