Author Archives: KirstieJane

About KirstieJane

Programme lead for open source Tools, Practices and Systems at the Alan Turing Institute, London, UK. A passionate advocate for replicability and reproducability in academic work and for the diversification of researchers in science. An ally to the LGBTQ family and tireless fundraiser for the AIDS/Lifecycle ride. The tags in my profile picture read: Fighter, Hero. War on AIDS. Rest stop no. 3. June 3rd, 2012 (Yes, its an old picture, but the mission remains!)

Foreign Policy’s 100 Global Thinkers 2016

On Monday 12th December my friend and collaborator Dr Petra Vertes and I were honoured in a list of 100 Global Thinkers by Foreign Policy magazine.


Petra Vertes and Kirstie Whitaker. Neuroscientists, UK. Named as Foreign Policy Global Thinkers for mapping the origins of schizophrenia.

Here’s what they said about us:

Mental illness often appears in adolescence. British scientists Petra Vertes and Kirstie Whitaker have found clues as to why in MRI scans. They examined some 300 young brains, noting that the “hubs” that connect different regions of the brain are still changing during the teenage years. Vertes and Whitaker then consulted the Allen Brain Atlas, which maps regions of the brain by gene expression, and found that the areas where the MRIs revealed the most change were those where genes linked to schizophrenia had the strongest expression. The discovery may prove an essential building block for future health research. “Knowing what happens in the run-up to the emergence of mental health disorders gives us the chance to build interventions and treatments that might prevent them in the future,” Whitaker told ScienceNode. (Photos courtesy of Petra Vertes and Kristie Whitaker)

It’s an incredible honour to be acknowledged for our work, but I do want to make something super clear: we didn’t do this on our own. You can see from the author list of our paper, published in the Proceedings of National Academy of Sciences this summer, that there are a whole bunch of colleagues who worked with us!


The title and author list from our paper (DOI: 10.1073/pnas.16017451130)

The NSPN Consortium on that author list is particularly important to me. It’s difficult to know who “contributed enough” to a scholarly work to warrant authorship, but with the consortium list we’re able to name all the research assistants, admin staff, graduate students and fellow researchers and acknowledge that good ideas come from a ton of hard work and wide ranging conversations.

The other folk to acknowledge are the Allen Institute for Brain Science who make all their amazing data openly available for anyone to use, and the 300 Neuroscience in Psychiatry Network participants who came in for brain scans. THANK YOU!

You can find out a little more about our work in this lovely Data Story from the Allen Institute.

Petra and I had tonnes of fun in DC. We were part of a round table discussion on the “three biggest problems facing the next president”. We discussed challenges related to demographics, economics and security.

The schedule for our Global Thinkers brainstorming session.

You’ll see from the pictures below that we were all in a circle. The Foreign Policy CEO David Rothkopf really emphasised his desire for a diversity of thought in the discussion.

We had a catchbox that meant as many people as possible were able to speak, Washington locals and global thinkers alike.

Brainstorming Session 1
Brainstorming Session 2

Brainstorming Session 3

Brainstorming the challenges that will be faced by the incoming US presidential administration.

And then of course, there was the actual awards ceremony. Here are two pictures I’ve stolen from Michael S Smith II who was included in the list for his work “bridging the government-hacker divide”. (So. Great. His work reminded me of that done by the awesome Mozilla Open Web fellows.)

On stage listening to all the incredible thinkers describing their work. Picture credit: Michael S Smith II via Twitter

Our view from the stage of Foreign Policy CEO David Rothkopf addressing the invited guests. Picture credit: Michael S Smith II via Twitter

I can not recommend to you more strongly to read through the 2016 100 Global Thinkers list. Everyone on there is a truly exceptional person doing such good in the world.

The list is very well balanced for gender, and there are a large number of thinkers who people of colour. There’s also a good representation of people who live and work outside of the USA. This wasn’t a coincidence. In his address, the CEO and editor of Foreign Policy, David Rothkopf, pointed out that ensuring there were great women on the list was a priority. His point, and I agree, is that this change won’t happen without conscious effort.

On that point, I want to highlight something that was really special. Foreign Policy flew Petra’s husband, Naaman, and 6 month old son, Noah, out to Washington DC to make sure that she was able to attend the event.

Foreign Policy put their money where their mouth is by ensuring that new mum Petra was able to attend the event. They flew her husband and 6 month old son out to Washington DC.

Our paper came out just a few weeks after Noah was born and so Petra has been on maternity leave for all the publicity and media attention that it garnered. She’s having fun with her amazing son, but she’s also missing out on some of the credit that she should receive. For example, in a perfect world the interview with the Allen Institute above would have been with Petra as linking the MRI to genetics and Allen Institute data was her work.

I’m so glad that Petra and I were able to celebrate together. And I’m still overwhelmed that our work was recognised in such a positive way. Here’s hoping the Neuroscience in Psychiatry Network team, and other researchers around the world, can continue to understand the emergence of mental health disorders and make a difference in the lives of young people at risk around the world.

Petra and me. Global Thinkers 2016!

Friday Tweet Collection – 10th July 2015

I wrote a great big long email to my lab mates this morning and I figured I’d share it here just in case my collection of tweets was of interest to others!

Please do share your own favourite tweets or news stories in the comments!

Happy Friday everyone,

I’ve been finding twitter very interesting over the last few days and thought I’d share some of the more interesting articles that have been popping up on my timeline.

Researchers find the organization of the human brain to be nearly ideal
This is in reference to this recent paper: Navigable networks as Nash equilibria of navigation games. It’s another paper I’d be interested to know your opinions on. If I’m being honest I read the brain section as a little over stretching the point but that’s likely to be strongly related to the fact that I don’t believe the DTI network they’re studying (Hagmann, 2008) is representative of how the brain is really sending messages. If you believe it though, then it’s a nice little fact to include in talks, introductions, grants etc. Networks FTW.

Family background influences clinical variability in #genetic neurodevelopmental disorders
This was re-tweeted by Dorothy Bishop (who is amaaaaazing. I loves her. You should know about her blog if you don’t already. While we’re at it you should also know about Athene Donald’s blog too.) This tweet drew my attention to the recent paper: Shift happens: family background influences clinical variability in genetic neurodevelopmental disorders. It basically argues that the “old-fashioned” splitting of psychiatric disorders into separable groups is not supported by recent analyses and that the abilities of your family members affect the abilities of children with genetic disorders – for example if parents have high IQ their child who has a genetic disorder is likely to have higher IQ (still low, but higher) than a child with an equivalent disorder whose parents have lower IQ. I think it’s a great reference for anyone who wants to understand how genes interact with the environment, brain function, how the brain changes and how different disorders overlap. Nature AND Nurture FTW.

Interesting perspective piece @NatRevNeurosci | Rethinking segregation and integration
This one was from Olaf Sporns and is an opinion piece arguing that whole brain modelling is good and we should do it, or as they say we should be: Rethinking segregation and integration: contributions of whole-brain modelling. Since we’re already doing that then really I suppose we can just pat ourselves on the back. But maybe it’s another useful reference for grants etc.

Come to Musical Celebration of #womeninscience All profits to @Science_Grrl w/ @Timothy_Bussey
I can’t make this night of music and fun at Portland Arms tonight (10th July) at 8pm because I’m babysitting my godson but I’d strongly encourage you to attend. There are 5 bands, including a few Cambridge Neuroscience acts and it’s raising money to support girls and women in STEM fields (£10 entry).

Really looking forward to the @CamBrainCNS Art Exhibition on 11th July at 6pm. Join us at St Barnabas church
This one was from me – I will be attending the first CamBRAIN art exhibition on Saturday at 6pm. It’s going to be gorgeous, you should come along 🙂

Former Google and Apple exec calls on women to stop saying ‘just’ at work
This article points out how many times women (more than men) use the word “just” in their daily communications and calls it out as a “permission” word and a “child” word. “Could you just take a look at this? Just wondering if you’d managed to look at my email.” It perpetuates a stereotype of women in submission to men and is something we can easily change. Just ctrl+f every email and ask if the j-word needs to be there.Usually a shorter sentence gets the point across more easily!

HA – she says – having written the most monster email of all time.

I know that some of our lab are organizing a conference in September….is there any information available for it yet? I’ve been emailing with Martijn van den Heuvel and he asked if I would be there….and I realised that I didn’t know but would very much like to attend!

Update: You can find the information for the Connectome Workbench | Brain networks at micro- and macro-scales conference here. It will be held in Cambridge on 11th and 12th September 2015 and you can contact Mr Manuel Schroeter for more information.

Happy Friday everyone! (I already said that but it bears repeating)

How to use the FSL and Freesurfer mailing lists for success in your PhD

FSL is the FMRIB’s Software Library, one of the most widely used neuroimaging analysis packages in the world, and is developed and maintained by the members of the Analysis Group in Oxford. If you visit this ipython notebook you can see my calculations for how many emails were sent on their mailing list in April 2014: a mind blowing 871!

Freesurfer is another extremely popular tool developed by the Laboratory for Computational Neuroimaging at Massachusetts General Hospital in Boston. I haven’t calculated all the emails from their mailing list, but there were 41 on a representative day in December (yesterday) so I think I can safely conclude that those researchers aren’t sitting about doing nothing either.

Although anyone can reply to emails on the list, there are a small number of developers who will most likely to reply to your email, and the number of answers that they provide on a (literally) daily basis is awe inspiring.

They want you to use their tools, and the very first email to the FSL list said it all:

First FSL list email

The very first email to the FSL mailing list. Screen capture on May 17th 2014 from

If you think about it, there’s a really strong chance that – even in just one month – someone asked a question that’s relevant to you:

  • Are you learning a new neuroimaging analysis technique for the first time?
    • So have thousands of others before you!
  • Are you unsure about your statistical analysis plan?
    • So were thousands of others before you!
  • Are you confused by an error message?
    • Thousands of others before you have stared at the words “child process exited abnormally” with absolutely no idea what went wrong and I suspect many more will in the future.

My point, as I’m sure you’re getting, is that there are very few new questions. So rather than just jump in and ask someone, it’s your job as a new scientist to learn from those who have come before you.

I would put the most helpful emails broadly into two categories: understanding error messages, and understanding statistical models. If you’re getting an error message when you run FSL, you probably aren’t the first person to see it. It’s almost guaranteed that someone else has had the same difficulty as you, has asked the question before, and has received help. And while your statistical model will be specific to your data set, there are almost certainly analogous models that have been used in the past.

All the information is in those mailing list archives, just waiting for you to help yourself.

So, here’s what you have to do:

  1. The FSL and Freesurfer mailing lists are very difficult to search, so step one is to subscribe to the lists and create your own archive. I use gmail and find that searching the 7 years of archives (I’ve been at this for a while) in my account makes finding appropriate emails much easier.
  2. Read the subject lines of all the emails. I’m in the UK and tend to wake up to a lot of emails from the USA, so I have a little zen moment every morning where I archive all the FSL and Freesurfer emails from my inbox. Given that I’ve been reading the emails for a long time I tend not to read many, but when I see something about a new feature, or a question that seems like something that might be relevant then I go to step 3…
  3. Read the emails that might be interesting and bookmark those that are useful. If you see someone asking about a problem with dtifit and you know you’re going to be conducting DTI analyses then read that email. Even if it isn’t a question you have now, there’s a good chance it’ll be relevant in the future. If it really makes sense then bookmark it so that you can easily find it in the future. You can do this in gmail either with clever use of labels etc, or I often just email it to myself with a bunch of words that I’m likely to try to type into the search bar when I look for it in the future.
  4. Read all emails about statistical tests that you don’t understand and try to answer (in your head) each person’s question before you read the expert’s answer. These are prime learning opportunities, and there are profound similarities across all tests. Use these worked examples to hone your understanding. Talk through ones you don’t understand with friends and colleagues. Create a database of examples that are useful and refer to them often.

If you do have to send an email to the list make sure that you’ve done your due diligence: search through your archives, and the general mailing list archive for your particular error message and make sure you completely understand all the statistical examples on the appropriate help pages, including, but not limited to: these FSL GLM examples, Jeanette Mumford’s advice on demeaning covariates and these Freesurfer GLM examples.

Only once you’ve convinced yourself that a simple LMGTFY search won’t give you the answers you need, then you can write your email to the list. I don’t want to paralyse you with fear, but thousands of people will read that email: make sure you look good while you’re asking your question!


  • Make sure your email is polite – these people are busy and not paid anywhere near enough for their jobs. A little courtesy goes a long way.
  • Explain concisely what you want to do and where the problem is. Don’t put in more detail than you need, but do make sure that someone can follow your question easily.
    • If you’re asking for help with an error message include the full error screen printout and the command you typed before it appeared!
    • If you have a problem with viewing an image then take a screen shot and annotate it to point out exactly what you’re worried about.
  • Include in your post what you’ve tried and what resources you’ve exhausted. If there’s an old email on the list that you found but didn’t understand, cite it. Show the readers that you’ve done some work towards answering your own question.
  • Give your email a sensible subject line so that others can learn from it. Just think of all those times that you’ve read others’ questions and consider this your way of giving back to the community!
  • Before you send the email, do one last search in the archives. If you’ve gone through all these steps to make your question really clear, you may find that you can search more appropriately and those answers may be there ready and waiting!

It takes a while, but if you keep at these lists for a while you’ll start to see what I’ve already told you: there are very few new questions it’s just a case of knowing what to search for.

If I were running a start up I’d strongly consider hiring people who had successfully completed a PhD in any discipline because I know that their Googling skills are among the best the in the world. It may not seem like “doing science” but figuring out how to find information from a variety of sources is fundamental to your success as a critical thinker. Research isn’t just standing on the shoulders of giants, it’s finding your way up to there in the first place!

After a while, you’ll be able to answer some of the questions yourself, and you can either transfer that understanding back to the email list, or at least be able to help your colleagues out.

Good luck, you got this.

Policies for Supervisions at Cambridge

Firstly, what on earth is a supervision?

Supervisions are in depth discussion groups that supplement each lecture course for undergraduates. These are very small groups – between 1 and 3 students – that are lead by a researcher at the University who works in an associated field. For example, I’m a postdoc in the Department of Psychiatry, my PhD is in Neuroscience but I teach Experimental Psychology. I don’t have advanced expertise in every topic covered in the undergraduate course, but I learn a lot through the supervision discussions, the lecture notes and the great world wide web. And of course, when structural and functional MRI, experimental design, brain development, reasoning, intelligence and mental health disorders pop up I get to share lots of the things that I’ve learnt along the way.

In fact, the most important skill that you develop in an undergraduate degree is critical thinking, and that’s what a good supervision will inspire. You can’t hide away, and you can ask anything you want. My favourite exercise is linking stories that have been in the news with lecture notes and the students’ own experiences. The essays that students write each week are particularly good at clarifying and communicating this knowledge and understanding.

Why do I supervise?

In increasing order of importance:

  • M.O.N.E.Y. Yes, I’m paid to supervise. But trust me, I’m not paid very much. There are almost no supervisors who are in it for the cold hard cash.
  • CV Enhancement & Career Development This is an important one, postdocs aren’t students anymore and many of them will be on their way to becoming lecturers, which means they’ll have to set up their own courses and teach large groups of students in the future. Supervising is an invaluable opportunity to understand which topics interest students at various stages of their undergraduate degree, which they find particularly challenging, and how they can better be supported in their studies. Moreover, if I were hiring a new lecturer I’d definitely want to see that they had already been explaining their field of study to small groups of students before they were let loose on a whole lecture theatre.
  • Desire to Educate You quite simply don’t supervise or teach if you don’t want to help others to learn. Lectures can be rather dense and difficult to follow and supervisions are the perfect opportunity to stay on top of your workload and fill in any gaps in your understanding. I like seeing students improve and succeed, and if I’ve helped in some way that’s even better.
  • Passion for the Subject I want to teach Psychology because I love Psychology (and Neuroscience) and I really value the skills that students of this topic acquire. I love the intersection between critical thinking, statistics, practical experimentation, self awareness and philosophy. I think it’s so easy to get excited about the human brain and the human mind and supervisions are a fantastic opportunity to engage the next generation (you) in all of these topics.

What should you expect from a supervision with me?

I really hope that you should expect an engaging discussion in which you have the opportunity to ask questions about anything you didn’t understand in the lectures, and hone your understanding by answering your peers’ questions. If there’s anything you don’t understand just put a star next to the topic in your notes and we’ll figure it out together in our supervision.

We’ll also spend some time going over your assignments (usually essays) and sharing feedback on how they can be improved. These assignments are taken from or inspired by past papers and they’ll both prepare for the end of year exam and test your understanding as we go along.

Finally, we’ll discuss any other topics in Psychology you might be interested in. This is really as broad as it can get, and is the magic pixie dust that can really transform a supervision into a fantastic learning experience. Bring me news stories, journal articles, anecdotes, philosophical ideas and we’ll talk through them. I’ll usually have some things that I’m interested in to talk about, but everyone’s lives are more exciting if you bring some questions and ideas to the table.

What are my rules?

I really only expect us to all treat each other with respect.

Your supervisions don’t count towards your degree grade so you could technically just not come along or not hand in any assignments all year and so long as you do well in the exam, you’ll be just fine. However, you’ll give me a giant headache and you’ll be running a pretty big risk that the exam will take you by surprise at the end of the year. Please simply 1) tell me if you won’t be at the supervision, 2) hand in your work on time and 3) join in the conversation and all shall be well.

Having said that, I’m really strict on that middle one so I’ll say it again: hand in your work on time or I will not read it. You must hand in assignments to the Department of Psychology “W” pigeon hole by 12 noon the day before your supervision. If you’re late and there are still essays there – well done! You’ve dodged the deadline and I’ll never know. If they’re gone I won’t read your essay. Full stop.

Please print out your assignments if you have completed them on the computer and number and put your name on every page. If you completed an essay under time constraints or closed-book please also include that information at the end so that I can adjust my grading appropriately.

I will always grade any extra credit work within 1 week of you handing it in. If you miss the week’s deadline I won’t read that essay, but I will read any other of your choice. Alternatively, if you want to complete any extra work – past paper questions, short answer questions, practical paper question – simply for more practice and feedback I’ll grade any and all of it. Please send me an email if you’ve dropped any work off into the Department of Psychology “W” pigeon hole so that I know to go and check.

You get two get out of jail free cards for the year. These really should be used for when you aren’t well, and you’re playing with fire if you use them too early in the year. The chances that you won’t have a cold in the Lent Term is low. They’re there to use at your discretion if you miss handing in an assignment on time.

If you’d like to reschedule a supervision please ask ahead of time. If you need to join another supervision time for a one off that’s usually fine, I’ll have to ask the other students but to date I’ve never had anyone complain. If you can’t make any of my scheduled times then you can ask for a different time but I can’t guarantee that I’ll be able to accommodate you. Ask politely, and justify your need and I’ll do my best. Demand it after missing a supervision with no notice and I’ll be much less likely to find another time.

If you don’t hand in an assignment on time, don’t hand in a replacement and you’ve used up your two get out of jail free cards, then I’ll ask you to spend the hour of the supervision writing an essay of your choice. It isn’t fair for the other members of the group who have completed the work that you benefit from the supervision without doing the same. Please, please do not put me in this position. It forces me to treat you as a child and I really don’t want to. Just hand in your work on time and we’ll all be happy.

As I mentioned at the beginning – your supervisions don’t count towards your degree – so the only thing I can do is report non-attendance or not receiving assignments to your Director of Studies. This is the equivalent of “telling your mummy on you” and is another step I really don’t want to take. I will always warn you before contacting your DoS and I do hope we can avoid any big dramas. If you have any serious concerns that you think I should know about, please tell me in advance. I’m very happy to work with you. As I said at the beginning, I really do like to see students succeed.

I want to end on a positive note

Supervisions are fun. Psychology is eminently interesting because it’s basically the study of yourself and others. It’s a mix of setting the world to rights over a pint with your friends and marvelling at how much we know of the most complex “machine” known to man.

Science isn’t static, there are a few pretty well established facts (the frontal lobe is at the front of the brain, the retina responds to light) but the details are still being refined. By the end of the year you’ll be able to pinpoint the nuances of many experiments and their limitations. And maybe you’ll even go on to contribute your own findings?

Why I would like to attend OpenCon 2014

I just submitted my application to OpenCon 2014 and, in the interest of openness, I thought I’d publish my answers to their questions here! Do let me know what you think, either here or on twitter @kirstie_j.

Please note that all the opinions stated here are my own and do not necessarily represent those of my employers. (I hope at least some of them do though!)

Why are you interested in attending OpenCon 2014? What is your interest in Open Access, Open Educational Resources, and/or Open Data?

In short, I’m interested in Open Access, Open Educational Resources and Open Data because the way in which we currently work as scientists is old fashioned and outdated. I would particularly benefit from the planned workshops and presentations concerning the position of postdoctoral fellows and early career researchers within the Open movement. During my PhD and postdoctoral years I have worked within large collaborative projects which means I do not have much power over the decisions that the team can make with respect to sharing the progress of the work. I have benefited greatly from “standing on the shoulders of giants” who put work they have conducted online, and I am passionate about ensuring I give back to future generations as quickly and efficiently as possible. I am concerned about how my work will be evaluated in the (hopefully waning) zeitgeist of “publish or perish [in top impact journals]” and would benefit from discussions of how to incentive openness for both junior and senior colleagues. As someone who has failed to replicate quite a substantial number of “widely held beliefs” in neuroimaging I would also appreciate a discussion of publishing null results and registration of planned analyses.

Are you currently involved in any projects, campaigns, or initiatives promoting Open Access, Open Educational Resources, or Open Data? If so, please describe the initiative and your involvement. If not, do you plan to promote Open Access, Open Educational Resources, or Open Data after OpenCon? How?

I am very proud to work within a large Wellcome Trust funded project – the Neuroscience in Psychiatry Network – which is studying how changes in brain development lead to the emergence of psychiatric disorders. We conduct genetic testing (blood samples), structural and functional brain imaging, and behavioural and cognitive analyses within a longitudinal framework. One of the stipulations of our £5 million strategic award is that we will make all our data available to the public at the end of the grant. These data will provide other researchers the opportunity to benchmark their findings against ours, to collapse datasets into larger analyses that cross cultural divides and re-analyse our data as new techniques are developed. We have maintained a strong focus on providing clear documentation, while ensuring the anonymity of the participants is strictly maintained.

I am particularly involved in the brain imaging analyses: my analysis code can be downloaded from my GitHub account ( and I use that platform for two primary goals. 1) To ensure that every step of my analysis can be recreated from scratch by another researcher. 2) To share the work that I have completed optimizing analyses with other researchers. The first goal is my way of ensuring that all the work I publish has a “paper trail” – there are so many decisions to make along the way for complex analyses of large data sets (which run to terrabytes in size) that the traditional methods sections in academic journal articles are too limited to accurately share every decision that is made. Where the first goal is about local efficiency and accountability, the second is a more general contribution to the global efficiency in science: ensuring that what is already known can easily be found, referenced and improved.

How do you plan to use your experience at OpenCon 2014 after the event?

I will use my experience to galvanise my peers and ensure that the work I am conducting within collaborations is shared to the best of our collective ability. I will continue to share my analysis code and I hope to learn how to contribute it to other projects. I hope that by attending OpenCon 2014 I will remain motivated to be part of this important movement to fundamentally change the way academia currently rewards researchers.

If you are planning to participate in Open Access Week 2014, please describe how.

I will use this week to finally publish a data set whose analyses have already been reported (Whitaker, NeuroImage, 2013). I will use Open Access Week 2014 as a motivator to inspire my collaborators to release as much of the neuroimaging data as possible without violating the anonymity conditions stated within participants’ informed consent. I will also publish the complete analysis code to accompany the paper. Both of these goals are ones that currently are not rewarded within my specific career track, but which I hope will help others within the field. 


Whitaker, K. J., Kang, X., Herron, T. J., Woods, D. L., Robertson, L. C., & Alvarez, B. D. (2014). White matter microstructure throughout the brain correlates with visual imagery in grapheme-color synesthesia. NeuroImage, 90, 52–9. doi:10.1016/j.neuroimage.2013.12.054


OpenCon 2014 program:

Right to Research homepage:

Open Access Week 2014 events page:

AIDS/Lifecycle 2014 Fundraising Campaign Launch


To celebrate Valentine’s day – the international day of love – I’m launching my AIDS/Lifecycle fundraising campaign. I need to raise $3000 to be allowed to ride 545 miles through California from San Francisco to LA, but I’m aiming for $5000. Lets see if we can bust through that target before June 1st when I start the 7 day adventure.

You can read more about why I ride here, but I suspect that this picture of my team from 2011 will tell you one of the reasons.


The money I raise will go to the San Francisco AIDS Foundation and the LA Gay and Lesbian Center to help them continue their great work supporting men and women in California who live with HIV. I think the mental health support that these charities provide is one of the most powerful aspects of their work, with their testing and education programs that are helping to reduce new HIV infections in close competition!

Please donate whatever you can. With your help, we can make a real difference in the fight against AIDS.

Thank you for your support

That link again:

Open Science: Peer Review

On 23rd December 2013 I received notification that the paper Bryan Alvaerz and I wrote, “White matter microstructure throughout the brain correlates with visual imagery in grapheme-color synesthesia”, was accepted to NeuroImage.

It was the best Christmas present.

The whole experience with NeuroImage has been excellent. We had good reviewers who were polite and thoughtful. Their comments have improved the manuscript and we were accepted after one round of revisions. In our letter to the editor we thanked the reviewers for their insightful comments and I almost included a footnote: “No, really, I mean it!”.

On 24th December I sat down and made sure to pay this forward. I was asked on 18th December to review a paper, and I wanted to make sure that it didn’t get forgotten in the Christmas rush. I was given quite a tight deadline (2 weeks) and I really wanted to encourage these sorts of speedy turnarounds from journals and other reviewers.

It really sucks to be left waiting once you’ve sent your baby out into the ether.

I’ve submitted the review now, but I’d like to keep a track of how long each of these processes take. I strongly believe that scientists should be rewarded for their reviews even if they are anonymous. Peer review is the foundation that all of academia is built upon, and while it has its flaws, there’s a chance that the system we have is the best we’ve got.

However, I’d like to contribute a little to the #OpenScience movement. And to that end, I’m going to make public on my GitHub account two CSV files. One, reviews_for_me, logs all of the submissions of my papers, and the other, reviews_by_me, logs my reviews and how long I took to send them in.

Once there are more than one entry in each I’ll make a little graph of the times to review.

Even if the least it does is keep me honest and motivated, that will be enough. And maybe, just maybe, it’ll encourage others to take as much care as those thoughtful reviewers Bryan and I had for our paper.

Question for Commander Chris Hadfield

Sitting at the table in the Netherlands talking to Chris Hadfield on Radio 5 live.

Sitting at the table in the Netherlands talking to Chris Hadfield on Radio 5 live.

I’m writing this while sitting listening to BBC Radio 5 live and preparing for my five minutes of overwhelming excitement that will happen in about 20 minutes. The producers of the Victoria Derbyshire show will call me at 10:30 and I’ll have the opportunity to ask my absolute most favourite person on the whole planet a question. Just one question. What on earth am I going to say?

What I love most about Chris Hadfield is how well he communicates with people, and what an exceptional role model he is to everyone back on earth. I know he’s answered so many questions already (check out his three reddit AMAs before, during and after his time on the international space station) and so I spent all of last night trying to come up with an interesting question that might not already have been considered.

Here’s what I came up with:

My name is Kirstie Whitaker, I’m a researcher at the University of Cambridge and I study brain development. I’m really passionate about encouraging the next generation of scientists to join STEM careers, and I don’t know of anyone who has fulfilled that mission better than you [Commander Hadfield]. If anyone hasn’t watched the experiment of what happens when you wring out a wet towel in space, you really have to google it now! (I think I watch it almost every week when I need to be reminded of the magic of what human beings have achieved!)

My question is: You receive so much training as part of the Canadian Armed Forces, CSA and NASA for all the challenges of living in space. Did anyone give you any advice on how to deal with becoming a celebrity? Did anyone predict that you were going to be such a hit? And how did your family react to your fame?

I has so many follow up questions that were related to this idea: Do you think there is additional pressure on future astronauts to fill your boots? Is there a responsibility for “federal employees” to communicate what they’re doing to the taxpayers? Did the ability to interact with millions of people come naturally or is it something you worked to improve?

There were a few off topic questions that my friends brought up too: Do your vocal cords work differently in space? Did you save off your mustache now that movember is over? Is your son single?

It’s somewhat silly to be so excited about being able to talk to your hero, but I’m running with it. I thought his answer to my question was wonderful, as were his responses to all the other questions. He talked about the psychological support that NASA provides, and how it stands in contrast to the very little support that the early astronauts received. He thanked his son for spreading his tweets to other social media forums, and pointed out that social media is just that: social. It was through these interactions with everyone down on Earth that he created such a wonderful feeling of community.

You can listen to the interview here.

Let me know what you think.

What would you have asked?

Reproducibility and Replicability

I am extremely passionate about both reproducibility and replicability in neuroimaging. Reproducibility is the ultimate goal, while replicability should be the bare minimum that we demand in the 21st century. To this end I am committed to releasing all the analysis code from my peer reviewed manuscripts. You can find it at my github page. Please do use whatever you find there, and let me know if you think it could be improved.

There is a strong distinction between replicability – which requires that others can recreate exactly what you did with exactly the same dataset – and reproducibility. Reproducibility is the ability to find the same general pattern of results in a different data set. Publishing my code is an important step towards this goal because it allows others to begin to reproduce my results in their own data sets. I strongly encourage collaborations with other MRI researchers who are seeking to answer similar questions about brain development. Findings that appear in both of our cohorts of young participants mean so much more than all the single analysis findings put together.