In which I get ready for Dawi to return to The Old World...
With The Old World bringing back two of my white whales from my childhood in the form of Bretonnians and Dwarfs I’ve had a lot of fun projects this year. I wanted to do a slightly different Dwarf scheme than the old green and gold I remember seeing in White Dwarf as a kid and settled on the old Zhufbar livery of white and light blue. It makes for a striking force on the table top and is relatively speedy to paint up as detailed below!
In which I finally start delivering on the promised painting guides...
I have been sat on a fully constructed Battle of Pelennor Fields box for just about a year after purchasing it as a Christmas present to myself at the tail end of 2021. Having signed up to a few "slay the grey" style challenges in the New Year I thought it was time to start with a nice easy paint job.
In which I modify an old family recipe to be vegan friendly...
After successfully turning my hand to vegan Christmas cake I thought it was high time I adapted my old Christmas pudding recipe to be vegan too.
In which I discuss getting the dominant colour from an image quickly...
I have recently made a Discord bot that searches for online versions of board games to help people find games to play remotely. This link will add it to your server.
Discord embeds have a colour bar down the side that can be manually set. I thought it would be cool to have this display the 'average' (i.e. dominant) colour of the board game box and decided to investigate the best way to do it.
In which I plan my holiday tasks…
So it may just be because it is 2020 or perhaps I'm just a bit lazy but I’ve found that I often start holiday breaks with a list of things I’d like to do and by the end of the trip* I’ve not achieved most of them. Whether it’s odd jobs or relaxing activities I wanted to get through I just accidental sit around and don’t do them. This holiday season I decided I needed a to do list and though I’d try out the new Todoist Boards feature.
*Or, let’s be real this year: sitting on the sofa at home.
In which I run through setting up a Python environment on Windows...
I'm going to preface this post by saying I'm not breaking any new ground here. As is often the case, though, a beginner wanting to set-up an environment to do this will have to go to multiple websites to collect this info so I'm going to distil it into one post.
I am going to talk about Python 2.7 as currently it has the most support for libraries. This method should work equally well for Python 3 but I have not tested this.
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).
In which I talk about fitness and the road ahead...
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.
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:
In 5 Years:
In 10 Years:
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
The thesis is currently 122 pages long with 29,206 words and 154,203 characters.
Tom Out!
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:
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.
In which I use MetaPost to generate publication quality pulse sequence diagrams...
Pulse sequences are the series of radio-frequency pulses required to generate an MR image. If you are an MR Physicist you will see these a lot and probably wondered how can I generate nice pulse sequences for my thesis, papers etc. Well handily using MetaPost and these files you can!
In which I review some floral green tea and update you on my life...
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 :)
In which I run through a useful tip that Microsoft managed to just miss explaining...
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...
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.
That tea review data in full...
So we set out to try all the major and supermarket brand teas and decide which was the best this year.
We tried the following teas:
Postdoc Fallacy
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.
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 "
" after all.
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.
I've added a links/cool stuff section to the blog which you can find here:
. It includes my very much under-development MRI glossary :)
Tom Out!
P.S.
http://www.vitae.ac.uk/researchers/1270/Careers.html
P.P.S.
How to Get 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.
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.
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!
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?
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.§
What can you expect from your time doing a PhD then?
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.
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.
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.
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.¶
VIVA
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 http://www.findaphd.com
¶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.
