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Dr MacLove, or How I Learned to Stop Worrying and Love Apple

tumblr_lvuw7pdsFg1r2r3c4o1_500Back in the 90s it was easy; if you were a graphic designer, or some kind of proto-hipster with a trust fund you used a Mac. Everyone else used a PC. Then in the 2000s Apple started making iThings, everyone started going absolutely batshit crazy over them, and suddenly Macs were everywhere as well.

I’ve used both in parallel since about 2003 – I started off with a G5 power mac as a desktop complemented by a Windows laptop, but that’s now reversed with a Windows 7 PC on my desk at work, and a MacBook Air. This shift was significant – the desktop is what’s provided to me by my job, the laptop is my personal computer; what I choose to buy for myself.  Despite using OS X since 2003 I only really started liking it when I got my first Apple laptop – a 2009 MacBook Pro. This was also around the time that I got an iPhone 3G, which seemed like some incredible advanced artefact from the future compared to the chunky ‘smartphone’ I was using before that ran Windows Mobile 6.5; an unbelievably awful OS which I could never get to work as it should. I’ve since swapped the Pro for a 2012 MacBook air, bought an iPad mini, and am on my third iPhone, so my conversion is pretty much complete. I’ve looked at Android ‘phones and tablets, honestly, I have. Some of them are very nice, but the OS just always seems too…  busy. Maybe it’s my age, but I just want something I can pick up and use without a massive learning curve. I’m happy to stand up and say I’m an Apple-guy, and it took a while, but I’m finally actually OK with that.

It took a while, but I’ve now found Mac versions or fairly close equivalents for all the software I used on my PC. At first I sometimes used to boot into Windows using bootcamp to use a couple of applications, but I deleted the partition a while ago – I just wasn’t using it anymore. I probably won’t be spending money on any Windows machines for the foreseeable future. I know that Mac vs. Windows is one of the most hackneyed, pointless and bitter debates on the entire internet, but I just couldn’t resist setting my own bit of troll-bait out. Here, then, are the major reasons I became a Mac convert – your mileage may vary, personal opinions only, blah blah.

The MacBook Air
The Air is the machine that kicked off the ultrabook trend and, to my mind, PC manufacturers have still yet to equal the Air’s amazing combination of power, usability and portability. My 2012 model is greased-lightning-off-a-shovel fast – it chews through a set of fMRI pre-processing twice as fast as my old MB Pro, and that was no slouch either. The 2013 models are even faster, with better graphics and a frankly ridiculous 12-hour battery life. If you can live with a relatively small (128/256Gb) amount of storage, it’s a peach of a machine. Plus, I can carry it around all day and barely even notice the weight. For my money, the Air is the best value computer out there – I don’t think the step-up in performance you get with the Pro is worth the price, personally.

The Apple Trackpad
Using the trackpad on a Windows laptop feels like going back to the stone age after you’re used to the fantastic set of multi-touch gestures on an Apple laptop. Have never found one on a PC that even comes close.

Migration Assistant
Remember the excitement of getting a new computer and then the agony of re-installing all your applications, and tweaking the system to get it the way you like it? That pain doesn’t exist for me anymore. Apple’s Migration Assistant lets you do a time-machine back-up of your old computer on to an external  drive, plug that into the new one and everything is reproduced; your applications, desktop, OS settings, bookmarks, everything. It’s awesome.

Expose/spaces
OS X’s system of virtual desktops is brilliant, and essential for me, now that I’ve got used to it; flipping between desktops with ctrl+left/right arrow keys is fast and smooth, and means you can really extend the limits of what can be done on a 13″ laptop screen. I have no idea why Windows doesn’t implement virtual desktops.

Unix
In the last couple of years I’ve switched to using FSL as my main fMRI-analysis platform. FSL is developed on Macs, runs well on other Unix systems, but needs some kind of unix-emulation to run on Windows. Urgh – forget it. I do like being able to open up a terminal and institute little tweaks to the OS and applications as well. Of course Matlab/SPM and BrainVoyager also run beautifully on OS X.

Installing/Uninstalling
To install an application on OS X you drag it to a folder. To uninstall it you drag it to the recycle bin. That’s it.

Mac-only software
Osirix is without any shadow of a doubt, the best free DICOM image viewer available, and it’s Mac-only. Other things like Automator I’d really miss too, plus of course Apple’s super-fast and comprehensive spotlight search is awesome.

No crapware
You know all that shit you have to uninstall as soon as you get a new PC? Free trials of anti-virus software, media players, desktop icons that link to shitty Yahoo services you have no intention of ever using? Doesn’t exist in OS X.

 

Having said all that, of course there are annoying things that drive me crazy about OS X too. No system is perfect after all…

No Cut/Paste
You can copy and paste files between two file locations, but you can’t CUT and then paste. Seriously Apple, is this really a problem?

Annoying behaviour of the green button
The green button at the top of the window that I still think of as the ‘maximise’ button – it’s annoying. It seems to re-size the window pretty much randomly. I hate it.

ITunes
For the love of all that is holy Apple, will you please do something about the benighted clusterfuck that is iTunes? It’s utterly heinous.

Feel free to disagree with me in the comments. If you think Windows 8 is the greatest OS ever devised, please say so. Personally I think it’s a botched, compromise that tries to bring touch-functionality to laptops and laptop-functionality to tablets and does neither well, but hey, that’s just my opinion. Windows is like Star Trek movies – every other one in the series is decent, which means Windows 9 should actually be pretty usable.

Anyway – flame on!

The effects of hardware, software, and operating system on brain imaging results

A recent paper (Gronenschild et al., 2012) has caused a modicum of concern amongst neuroimaging researchers. The paper documents a set of results based on analysis of anatomical MRI images using a popular free software tool called FreeSurfer, and essentially reports that there are (sometimes quite substantive) differences in the results that it produces, depending on the exact version of the software used, and whether the analyses were carried out on a Mac (running OS X) or a Hewlett Packard PC (running Linux). In fact, even the exact version of OS X on the Mac systems was also shown to be important in replicating results precisely.

Figure 3 of Gronenschild et al. (2012) showing the effect of different versions of FreeSurfer on obtained grey-matter volume results. Percentage scale at the top, p-values on the bottom.

The fact that results differ from one version of FreeSurfer to another is perhaps not so surprising – after all, we expect that newer versions of software should be ‘improved’ in important ways, otherwise, what would be the point in releasing them? However, the fact that results differ between operating systems is a little more worrying – in theory any operating system capable of running the software should produce the same result. The authors recommendations are that 1) Researchers should not switch from one version/operating system/platform to another in the middle of a research project, and 2) that when reporting results software version numbers, and the workstation/OS used should all be documented. This seems broadly sensible.

It got me thinking about neuroimaging software more generally as well though. In general, people don’t do detailed evaluations of software of the kind reported by Gronenschild et al. (2012).  As an enthusiastic user of several fMRI-related packages (I’m currently using SPM, FSL and BrainVoyager, all on different projects) I’ve often wondered what the real differences were between them, in terms of the results they produce. Given how many people around the world use brain imaging software, you might think that some detailed evaluations would be floating around, but in fact there are very few.

I think there are several reasons for this:

1. It’s (perhaps understandably) regarded as a waste of time. After all, we (meaning researchers who use this software) are generally more interested in how the brain works, than by how software works. Neuroimaging is difficult and time-consuming and we all need to publish papers to survive – it makes more sense to spend our time on ‘real’ brain-related research.

2. Most people have one (or at most two) pieces of software that they like to use for neuroimaging, and they stick with it; I’m somewhat unusual in this respect. The fact that most people use just one package more-or-less exclusively means there’s a dearth of people who actually have the skills necessary to do cross-evaluation of packages. Again, this is understandable – why take the time to learn a new system, if you’re happy with the one you’re using?

3. The differences between the packages make precise comparison of end-results difficult. Even though all the packages use an application of the General Linear Model for basic analysis, other differences in pre-processing conceivably play a role. For instance, FSL handles the spatial transformation of functional data somewhat differently to other packages.

Having said that, there have been a few papers which have tried to do these kind of evaluations. Two examples are here (on motion correction) and here (on segmentation). Another somewhat instructive paper is this one, which summarises the results of a functional-imaging analysis contest held as part of the Human Brain Mapping meeting in Toronto in 2005; developers of popular neuroimaging software were all given the same set of data and asked to analyse it as best they could. Interesting stuff, but as the contestants all used somewhat different methods to get the most out of the data, it’s hard to draw direct comparisons.

If there’s a moral to this story, it’s that (as the recent Gronenschild et al. paper demonstrates) we need to pay close attention to this kind of thing. As responsible researchers we cannot simply assume our results will be replicable with different hardware and software, and detailed reporting of not just the analysis procedures, but also the tools used to achieve the results seems a simple and robust way of at least acknowledging the issue and enabling more precise replicability. Actually solving the issues involved is a substantially more difficult problem, and may be a job for future generations of researchers and developers.

See also:
My previous post on comparisons of different fMRI software: Herehere and here.
Neuroskeptic has also written a short piece on the recent paper mentioned above.

TTFN.

In Praise of Hacking

A brief anecdote – last week I had to fix a website. Doesn’t matter which one, but there was a link that needed removing. Easy, you might think; not so, unfortunately. The link was embedded in a piece of malicious code in a website theme, which uses a bit of web technology called PHP. Now, I know very little about PHP, but I managed to find the right bit of code on the server and opened the file, to be greeted with absolute gibberish – a totally unintelligible string of numbers and letters. A bit of googling revealed that the code had been intentionally obfuscated by encoding it in base-64 – sneaky. A bit more googling eventually turned up a base-64 encoder/decoder which made sense of it, I stripped out the offending link, and uploaded a new version of the file back to the web server (using this awesome online ftp client), which (miraculously) worked! Job done.

The point of this anecdote is that you can achieve a lot with computers with a tiny bit of knowledge and a lot of experimentation – or just hacking around. Read the rest of this entry