ImageJ and Volume Measurement

In which I describe the complexities of analysing 3D images...

3D image analysis just seems to be one of those things that is harder to do than I'd like it to be.

Before starting it is worth pointing out that with MRI you can acquire volumes in two ways - traditional 2D with multiple slices or a 3D scan. As far as this blog post is concerned these are the same.*

A common measure in clinical MRI is the volume of an organ or part of an organ. After all when someone has brain cancer - "How big is the tumour?" can be a very important question. Here are my experiences of trying to measure volumes on MRI images.

*There are differences between these two methods of acquisition but that would require a whole blog post on it's own.

2012 in Review & New Year's Resolutions

In which I look back on a year (ish) of blogging and look ahead to 2013...

That Was The Year That Was!

Firstly WordPress have provided this nice summary of my year in blogging:

So this is my first proper year of blogging (I posted a few things before but wasn't really regular at all). It's been a lot of fun and I'm definitely here to stay :) I've managed the majority of my 3,000 odd views this year :)

Let the summarising commence!


I've messed about with Linux and Windows. I upgraded to Windows 8 and enjoyed it (it hasn't pissed me off yet!). I've also spent a fair amount of time learning $latex LaTeX$.


The main event was Project Thor which was a lot of fun and helped keep me in shape.


I didn't do much in the way of Airsoft this year :(


Due to foolishly agreeing to bake a cake for every CAOS rehearsal in order to become Social Secretary I have baked a lot of cakes this year. Also there was the annual Pudding Party!


I've had a placement at AstraZeneca which has been very useful and is still on going. I've also started looking into PostDoc options.


I reviewed a board game based on a TV show you might just have heard of. I also made an advent calendar full of alternative Christmas songs :)


I drank lots of tea and so it was a good year :)

I got featured on which was awesome! This is thanks to the Great British Tea Test 2012 :)

On to 2013!

Having survived the apocalypse let's have a few New Year's Resolutions:


I'll keep tinkering. No particular promises here but expect some more $latex LaTeX$ and Linux stuff along with anything interesting I find out :)


  • There will be some cryptic updates to Project 0 soon!
  • ManSSAGO is hosting the Manchester 2013 Cartoon Rally in February which I intend to have a costume for (I'm thinking Inspector Gadget).
  • Project Reynolds has a slight delay due to the party being moved back. This Project will be finished by mid-February.
  • I intend to get down to 13 stone for Project Reynolds and then down to 12½ stone by October.
  • There will be more sotumes later in the year :)


  • I will definitely airsoft more next year!
  • There will be some site reviews!


I'm 'contractually obliged' to make cakes until March sometime once a week so expect more cake making. It'll give me an excuse to use my new Mason Cash mixing bowl and silicon utensils :D


  • I'll finish my placement at AZ.
  • I will get a paper written (and hopefully published).
  • I will collect all of the data!
  • I will probably decide on PostDocs/future plans.


I'm expecting to get the following things* to review next year:

*I should go on KickStarter less!


Armed with my trusty new leaf tea, teapot and a new review style I will continue to drink lots of tea!

Tom Out!

Afternoon Infusion

In which I get a free tea with my pumpkin and ginger cake from Graze...

I recently got a few free Graze boxes and they send you a small piece of cake with complimentary tea :)


"A blend of assam and kenyan leaves."

There were no instructions so I used my usual 5 minutes brewing time and added a little milk.


Lighter than my standard teas but still a light brown, tea colour.


There is a hint of bergamot but the predominant aroma is that of black tea.


This is a very pleasant blend. Perhaps it's a gateway tea to those who don't currently like Earl Grey as it tastes like normal tea with a hint of bergamot. It is very refreshing and a great way to start the afternoon. The fact that it comes packaged with cake doesn't harm it either!

BII Showcase

This week I attended the 4th annual Biomedical Imaging Institute Showcase. It was very interesting to see new MR applications and to see a study that I was a subject in being presented. Also I managed to get the annual free mug, which of course I can now use to drink tea!


A refreshing afternoon blend which comes with a cake :) Lovely.

I know I've said this before but I think I may soon change the layout of my tea reviews as they are getting a little repetitive :S


Tom Out!

Bonus: M&S Turkey Feast

M&S sandwich
M&S sandwich

This week it is time for the king of the Christmas sandwiches IMHO - the M&S sandwich! Will it retain it's crown?

Price: £3.00

Taste: The stuffing is very tasty, you can taste the sage & onion. A small amount of mayonnaise makes the sandwich moist enough without overpowering. It could do with a bit more cranberry sauce but when you get a whole cranberry it is splendid. The turkey has a lot of flavour as opposed to in the others to date where it was indistinguishable from chicken.

Conclusion: Still excellent and the best so far. Will another sandwich topple it in the following weeks?

Postdoc Options

In which I discuss my thoughts on a career in research at the present time. In which I cover the options open to me both from a research point of view and location.

I still currently plan to have an academic research career as opposed to an industrial research career but I'm open to the possibility my AZ placement may change my mind.

A Career in Research?

So far I've enjoyed my PhD and the working environment that is academia. There are always problems with any working environment but I've only encountered minor niggles so far and there is a lot of freedom to carry out your work in a manner that suits you (as long as it gets done :) ).

From the few people I've spoken to about Postdocs so far it is clear that getting at least one publication published by the end of my 4 year programme is a must. While it is possible to continue my research career without a publication under my belt it will make applying for good jobs significantly easier. This is the world of "

Publish or Perish

" after all.

Location, Location, Location

There is a general rule in research - move! The majority* of academics suggest you change institution between PhD and postdoc (the same has been said about undergrad to PhD too) unless you truly are at the best institute in the world for what you are doing. This, of course, gives me something to start ruminating about and also a great opportunity to visit a completely new city for several years.

Obviously the UK† is always an option but this is probably my best opportunity to live abroad for a short while.‡ And there is quite a lot of choice open to me. With my current language skills I could easily look at Australia, Belgium, Canada, France and the US. If I learn one of the two languages I most wish I knew then I'd open up opportunities in Germany or Japan as well.

I've also been told that, besides English, the best languages I could be learning at the moment for research are Chinese (Mandarin) and Japanese. This definitely gives Japan some bonus points. Not only is it a very interesting place that I've always wanted to visit but if I'm going to invest the time in learning the language I might as well put it to use in that country.

*That I've spoken to.

†Unless something drastically changes I expect I'll always want to return to the UK. It's not just the tea, I generally enjoy it here.

‡Postdocs are usually a few years.

Changes to the Site

I've added a links/cool stuff section to the blog which you can find here:

MRI Glossary

. It includes my very much under-development MRI glossary :)

Tom Out!



CASE Placements and Research Software

In which I apologise for this week being low on blog posts and update you on my AstraZeneca placement. Also I use software I normally use for research for other purposes.I'm sorry there haven't been any updates this week. There was no cake made as I had no time for choir on Tuesday, no tea as it's an alternate week and the usual Thor update is delayed (pending a hot wire cutter).

CASE Placement

This week I started my work placement at AstraZeneca, the industrial part of my Industrial CASE PhD (see my post on PhD types). Apart from the system shock due to waking up significantly earlier than usual (my commute to UoM is a 15-20 min walk not a 45-60 min drive) the week has been good so far :) I've gone through a load of induction sessions and lots of positive feedback on my study designs and planning for the weeks ahead.

Next week I start work proper with my first study and hopefully the results will be as we predict. Sadly for now I can't give any more details due to confidentiality agreements. Rest assured though if I get a publication out of this placement (which I hope I will) it will be mentioned in this blog :)

Weeping Womble

On Monday night I managed to take a good set of photos of fellow Scout leader and Networker (Womble) walking ominously towards my camera. I used ImageJ a free, java based image tool commonly used by MRI researchers to animate this simple gif:

After fixing some timing issues, adding 'blinks' and a final word of warning I ended up with this final masterpiece of internet animation:

Proof that research software can be quite fun in your spare time!

Tom Out!

P.S. AstraZeneca

P.P.S ImageJ

Cool Physics #1

In which I describe some cool physics!So I thought I would start to impart any cool science/physics I've come across throughout my degree and continuing research. This post is going out while I'm at a conference - so this week have some beer!

Beer Bottle Fizz

When I came back from my first year at Uni a friend of mine asked me what Physics I had learnt that year. Casually I lifted by beer bottle and tapped hers on the top causing her beer to froth and foam over the top and down the side. She dived forward to stop any spillage (which as we all know is lick-age). Practically anyone who has been to a party involving alcohol has seen this trick - but how does it work?

Well why does the bottle fizz in the first place when you open it? Gas (C02) is stored in the liquid in equilibrium. When you open the bottle a new equilibrium needs to be established and so gas leaves the liquid and causes bubbles. When you hit the bottle you release a lot more gas compared to opening the bottle causing the bottle to fizz all over your hand/the table/a nearby cat. You can also obtain the same effect from slamming a bottle onto a table.

Smashing the Bottom of a Beer Bottle

Watch this video:

So how does that work?

Cavitation is mentioned but you've probably never heard of it. What happens is a vacuum is formed and then collapses very quickly. The force of the water crashing down through the vacuum is easily enough to break glass. In fact cavitation can be very damaging in things such as turbines:

The collapse of these 'bubbles' causes heating and shockwaves and causes lots of problems in devices such as turbines.

Tom Out!



Starting 3rd Year/So You Want To Do A PhD?

So I thought as my third year looms it might be worth reviewing my PhD experience and giving new or potential PhD students my thoughts.

2 Years In

So how do I feel now that I'm successfully onto the 3rd year of my programme?

In general, I am enjoying my PhD and I am very grateful for the opportunity I have been given. There are of course downsides but the majority are minor or would be the case in any job (such as delays beyond your control etc.). I am really looking forward to my upcoming industrial placement as it will be a nice change of pace and will (fingers crossed) lead to a publication.

As far as progress goes I could be a little further ahead but with the potential for publications this year and my first oral presentation at BC-ISMRM next week I'm very excited for my third year. There's always a bit of worry from being half-way through something but I'm coping well at the moment.

So You Want To Do A PhD?

There are already books[1] on getting a PhD but I think I'll summarise the general points below.

Why should you do one?

  • You want to get into academia/research - it's still the standard route.
  • You're really interested in a specific research area - if you enjoy it, do it!
  • You need a higher level qualification for your ideal job - though you still need to be interested!

Why shouldn't you do one?

  • Just for the title
  • Because you're afraid of getting a real job
  • You want to stay a student forever

So if you've decided you want to do a PhD there's still a lot of choice for doctoral courses, which one should you pick?

PhD Types

  • Traditional PhD/DPhil - Normally 3 years funded* (in the UK) and takes around 3.5 years, the traditional model with topic usually being set at the beginning by your supervisors. Funding from the research councils is currently £13,590 (tax free).†
  • EngD etc. - 4 years including taught elements and industrial placements.
  • DTC based PhD - usually 4 years with taught elements. Often you don't pick a research topic straight away choosing it between 3-12 months in.
  • Industrial CASE PhD - usually 4 years funded with a 3-6 month industrial placement. These include an increase to the normal PhD stipend of up to ~£7,000

I'm on an Industrial CASE PhD so there's the possibility I'm slightly wrong about the differences between the others.

Once you've decided your research field/topic, the type of PhD you want to do and double checked that your really want to do one - start applying!

Most PhD positions are advertised from January onwards with interviews around February. If there is funding though PhD positions need to be filled and there will be positions advertised all year. Summer tends to have a large number of PhD places which weren't filled early in the year on offer.§

So You're In For The Long Haul?

What can you expect from your time doing a PhD then?

1st Year

Regardless of your programme you are going to have to review the literature. This normally takes around 3 months and is sometimes publishable as a paper if your field is in an interesting niche.

You will learn how to use the lab equipment/computers/databases/blackboards you need for your continued research.

You will probably narrow down the topic area and methods to be used in future years.

You may get trained on something really specific (I was flown out to Bruker in Germany to learn how to program MRI scanners).

You will have some sort of report to get through to the next year. I had to have a full-on viva but other departments have a simple meeting with supervisors to see if you should continue.

2nd Year

This is usually your method development year. For CASE students you may go on your first placement.

If method development is quick you can start collecting useful data.

3rd Year

This is your data collection year. People on a '3 year' programme will need all their data pretty much by the end of this year.

4th Year

On a 3 year programme you will be writing the thesis until your agree viva date. On a 4 year programme you will finish data collection then write the thesis.


Graduate! :D

* This is for Sciences PhDs - it is a lot harder to get funding in the Humanities.

†Funding bodies will also pay your tuition fees.‡

‡I believe Wellcome Trust provide the best at the moment with total stipend of around £21,000

§You can see available positions on respective universities' websites and at

You will write a fair amount of certain thesis sections ahead of this time. Some people write up throughout and continue collecting data well into the traditional data collection phase.

Tom out!

[1] Phillips, E.M. and Pugh, D.S., 2000. How to Get a PhD: A Handbook for Students and Their Supervisors. 3rd ed. Maidenhead: Open University Press.


Polymorph mouldable plastic

So this is the first post of my new combined blogs *maniacal laughter*

One of the things I plan to post about a bit more regularly is my PhD. Not the general day-to-day stuff but the cool and wacky things that you wouldn't expect to do - of which there are many.

So I am in the process of prototyping various bits of MR safe equipment for use in my project and having been playing around with Polymorph. It is a re-mouldable plastic which you can melt in boiling water and then make into any old shape. For bonus cool science points it turns clear when mouldable and  white when it sets :)

Today I've been moulding it around an old tonic bottle and some test tubes - proof that my research will never cease to surprise me!

[You can buy Polymorph from Maplin]

Tom out!

P.S. This is my first Tinker post!

P.P.S. My blog has polymorphed!