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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.

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:

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.