PhD

Site Move in Progress

I've had a lot of headaches recently with WordPress failing on my blog and was already in the process of moving everything into one place on SquareSpace. With the recent complete failure of my WordPress theme (and several back-end issues) I have decided to initiate the transfer immediately. 

As the WordPress import is not perfect some posts will have issues I will be manually fixing in the next few weeks. If there is an issue a quick comment using the new Disqus system will bring it to my attention. Thank you for your patience!

Tom Out!

Fancy Thesis Tables in LaTeX: An Idiots Guide

Fancy Thesis Tables in LaTeX: An Idiots Guide

In which I provide a template for generating fancy, production quality tables for theses...

LaTeX as I've mentioned previously, is a document preparation system well known for its brilliant equations and can also be utilised to make very nice looking diagrams. The tables it generates, however, while neat are a little lacklustre.  This is aimed as a very simple guide to editing tables (regular LaTeX users may find this tutorial very basic).

Tom 3.5 & Life Plan 2014

In which I talk about fitness and the road ahead...

Tom 3.5

So once again I am unhappy with my level of physical fitness having let it slide a lot with work and other stress getting in the way. I need a new ridiculous goal but first I need to get back to my old fitness levels. I'm back on the old horse having started running everyday again and I've rejoined the gym. Expect a longer post in about 2 weeks time about how things are going.

I'm thinking my next "ridiculous challenge" should either be Tough Mudder or an ultra marathon (~40 miles not one of the 100 mile ones).

Why Tom 3.5? Well my last fitness drive was Tom 3.0. This isn't entirely a new leaf it's just me reminding myself to get back to what I was doing and hopefully take it further.

Life Plan (2014)

These are my goals for the next 10 years. I'm going to start posting the one year goals each January instead of having fixed New Year's Resolutions.

This Year:

  • Start learning Guitar (again)
  • Start learning Piano
  • Get a job
  • Finish my PhD
  • Don’t have a fat graduation photo
  • Receive my QSA at Windsor
  • Receive my DofE Gold
  • Write more short stories
  • Enroll on another marathon/Tough Mudder

In 5 Years:

  • Be earning £40k+
  • Be married or almost married
  • Have a published book
  • Have worked towards grades in Piano
  • Grade 5 music theory

In 10 Years:

  • Have children
  • Grade 8 Piano
  • Have several published novels

Procrastination

So I'm in full thesis writing mode at the moment but that doesn't mean I'm constantly writing. I do procrastinate (though usually with other jobs I need to get done) and this brilliant article explains why that's helpful: http://www.wired.co.uk/news/archive/2014-06/17/jorge-cham-phd

State of the Thesis

The thesis is currently 122 pages long with 29,206 words and 154,203 characters.

Tom Out!

20,000 views!

In which I discuss some blog stats...

Firstly thank you everyone who has come to my little corner of the internet to get me to this point. When I started off a little blog about tea 3 years ago I never expected it to be seen by anyone outside my group of friends. Secondly I actually ticked over 20,000 views about a week back but haven't had the time to write this post until now.

Word 2010: Footnotes and Mendeley

Word 2010: Footnotes and Mendeley

In which I discuss getting footnotes and Mendeley references to look nice in Word...

I may not have mentioned it before on this blog but I am a Mendeley advisor and a strong advocate of this free reference manager. In fact I cover the pros and cons of it in this video:

Data Drudgery, Steampunk Stark & Tepid Tea!

In which I discuss the borishness of data anlaysis, try an interesting new tea and lay out my next Tailor project...

Data? I 'ardly know 'er!

In a break from continuous Thesis writing I have recently been running another imaging experiment. This was, as you could expect, a fairly hectic few weeks with early mornings and late nights. It was, however, much better than the weeks following where I am now stuck with the unenviable task of analysing image after image in ImageJ. Regardless of your research area this is the boring part of a PhD - repeatedly doing the same thing over and over again. Hopefully there is light at the end of the tunnel though and this will be my final experiment - Great Success!

Now all I have to do is finish writing an 80,000 word thesis...

2013 in review

The WordPress.com stats helper monkeys prepared a 2013 annual report for this blog.

Here's an excerpt:

The concert hall at the Sydney Opera House holds 2,700 people. This blog was viewed about 8,700 times in 2013. If it were a concert at Sydney Opera House, it would take about 3 sold-out performances for that many people to see it.

Click here to see the complete report.

Proper Gradients for MetaPost Pulse Sequences

Proper Gradients for MetaPost Pulse Sequences

In which I improve upon the previous post...

In yesterday's post I talked about using MetaPost to generate Pulse Sequence Diagrams for MRI documents. I have been using this to make nice diagrams for my Thesis. There is one problem, however, with the pulse sequence file provided on Mark's website - it generates square gradients.

Osmanthus Green: Thesis, YouTube, Update!

Osmanthus Green: Thesis, YouTube, Update!

In which I review some floral green tea and update you on my life...

Thesis Writing

So thesis writing is fully under-way  now and my supervisors assure me that writing will get harder and longer as it continues - fun, fun, fun!

It takes me a while to get into writing but I expect I'll make a video about Thesis writing soon. I actually quite enjoy writing though so I hope I'll be able to keep the pace up and stay on schedule :)

Word 2010: How to Insert Numbered Equations Properly

Word 2010: How to Insert Numbered Equations Properly

In which I run through a useful tip that Microsoft managed to just miss explaining...

The Problem

If you, like me, are in the process of writing a long scientific document which requires multiple reviewers to be able to view changes you may sadly be saddled with using Microsoft Word.* Now, in defence of Microsoft, they have definitely improved the way Word works. Using track changes, Mendeley and with a little bit of tinkering you can have a passable writing experience and be able to send documents out for review by your supervisors. They've even included an equation editor that allows you to put equations in your document and save them for later use.

Sadly in formal scientific writing we often like things to look nice, pretty and numbered like this...

Warming Camomile & PhD 3rd Year Retrospective

In which I talk about my approaching final year and try a warming tea...

So in a few days I should be officially into my fourth and final year of my PhD.  That means I'm hopefully one year away from wearing these crazy robes...

MRI Basics: What Do I Need?

MRI Basics: What Do I Need?

In which I describe the components of an MRI scanner...

So following on from last week – other than a lot of money to pay for it all*, what do you need for an operational MRI scanner?

*Scanners are often upward of several million pounds.

A Large Magnet

In order to make a significant number of the spins in your body align in one direction a very powerful magnet is needed. The strength of these magnets is measured by a large unit called the Tesla (symbol: T). To get an appreciation of how strong that is there is another unit called the gauss which is also used to measure magnetic fields. 1 Tesla = 10,000 gauss and a normal bar magnet is around 100 gauss.

MRI Basics: What is MRI?

In which I explain the very basics of MRI...

Nuclear Magnetic Resonance (NMR) allows us to detect a signal due to a fundamental quantum property of atoms - spin (which I will explain in an upcoming post). Magnetic Resonance Imaging (MRI) uses these same principles to obtain images of (usually) hydrogen atoms in a substance/tissue.

(N)MRI is a non-invasive, non-ionising, imaging modality and is widely used in hospitals worldwide. What does all that mean?