Over the past couple of days, I have been archiving published fMRI projects, and copying data from SD cards to start new ones. I have written previously about ways in which I have copied and verified copied files, and this is a quick update to that post to document another tool for verifying copies.

As far as the copying itself is concerned, I still swear by Teracopy. As far as verifying that copies have been successfully made though, I have recently started using Exactfile. The tagline “Making sure that what you hash is what you get” sums up the procedure for using Exactfile, once you have installed it on a Windows machine.

Exactfile in action
Exactfile in action
  1. Create a single file checksum, or, if you are comparing all the files and subfolders within folders (even massive folders containing gigabytes of fMRI data) a checksum digest (illustrated above). This will be saved as a file using which you can…
  2. Test your checksum digest. You locate your digest file and the copied data you wish to compare against the checksums, and it runs through making sure each file is identical.

That’s it – pretty straightforward. Step 1 takes a little longer than Step 2, and if you’re comparing hundreds of thousands of files, you should prepare to have this running in the background as you get on with other stuff.

I am heavily reliant on Google Reader for how I keep up with scientific literature.

I have customised RSS feeds for PubMed search terms. I have RSS feeds for journal tables of contents. I access my Reader account on my work computer via the website, on my iPad with the paid version of Feeddler and on my Android with the official Google app. I use IFTT to and a Gmail filter to send everything I star for reading back to my email account so it can all get dealt with at work. It’s not perfect, but it’s efficient and it has taken me well over five years to arrive at this system.

And now, thanks to Google’s decision to kill Reader, I’m going to have to figure it all out again. That is, if Google Reader’s demise doesn’t kill RSS.

Right now, this video resonates with me.

If you’re trying to decide on a journal to submit your latest manuscript to, Jane – the Journal/Author Name Estimator, can point you in the right direction. This isn’t exactly breaking news, but it’s worth a reminder.

To use Jane, copy and paste your title and/or abstract into Jane into the text box and click “Find journals”. Using a similarity index with all Medline-indexed publications from the past 10 years, Jane will spit out a list journals worth considering. Alongside a confidence score, which summarises your text’s similarity to other manuscripts published in that journal, you’re also provided with an citation-based indication of that journal’s influence within the field.

Image

The other available searches are the “Find articles” and the “Find authors” search, the last of which I suspect I would use if I were an editor with no idea about whom to send an article to for review. As an author, it’s worth running abstracts through these searches too to make sure you don’t miss any references or authors you definitely ought to cite in your manuscript.

There’s more information on Jane from the Biosemantics Group here: http://biosemantics.org/jane/faq.php.

English: Extract from Raspberry Pi board at Tr...
The Raspberry Pi (photo credit: Wikipedia)

A few months ago, I suggested that Raspberry Pis could be used as a barebones experiment presentation machine. Since then I have got my hands on one and tinkered a little, only to be reminded yet again that my inability to do anything much in both Linux and python is a bit of a problem.

Fortunately, others with more technological nous have been busy exploring the capabilities of the Pi, with some exciting findings. On the Cognitive Science Stack Exchange, user appositive asked “Is the Raspberry Pi capable of operating as a stimulus presentation system for experiments?” and followed up at the end of January with a great answer to their own question, including this paragraph:

The RPi does not support OpenGL. I approached this system with the idea of using a python environment to create and present experiments. There are two good options for this that I know of, opensesame and psychopy. Psychopy requires an OpenGL python backend (pyglet), so it won’t run on the Rpi. Opensesame gives you the option of using the same backend as PsychoPy uses but has other options, one of which does not rely on openGL (based on pygames). This ‘legacy’ backend works just fine. But the absence of openGL means that graphics rely solely on the 700 mHz CPU, which quickly gets overloaded with any sort of rapidly changing visual stimuli (ie. flowing gabors, video, etc.).

Because of the lack of OpenGL support on the Pi, Psychopy is out (for now) leaving OpenSesame as the best cog psych-focused python environment for experiment presentation. The current situation seems to be that the Pi is suboptimal for graphics-intensive experiments, though this may improve as hardware acceleration is incorporated to take advantage of the Pi’s beefy graphics hardware. As things stand though, experiments with words and basic picture stimuli should be fine. It’s just a case of getting hold of one and brushing up on python.

UPDATE via Comments (1/4/2013) – Sebastiaan Mathôt has has published some nice Raspberry Pi graphics benchmarking data, which are well worth a look if you’re interested.
http://www.cogsci.nl/blog/miscellaneous/216-running-psychological-experiments-on-a-raspberry-pi-with-opensesame

IFTTT, if this then that, is an online, multi-service task automation tool I first read about on Lifehacker last year. I finally started using it today, and am seriously impressed.

IFTTT

Once you’ve signed up for an account, you can create IFTTT ‘recipes’ to check for actions and events on one online service (e.g. Google Reader, Dropbox, WordPress, Facebook etc.) and use them as an automatic trigger of a predetermined action in another (e.g. Gmail, Google Calendar, Tumblr etc.)

Example: To keep track of journal articles I should read, I monitor journal table of contents RSS feeds and e-mail interesting posts to myself for later download and consumption. I use my iPad, my phone, and occasionally my PC browser to access Google Reader, but struggle with how fiddly it is to e-mail myself on my mobile devices (with my filter-trigger keywords in the message body) whenever I find an article I want to read.  I’m sure I’ve missed articles I ought to have read through setting my action criterion a bit too high, as a direct result of how annoying it is to e-mail myself articles using the various Google Reader interfaces on my mobile devices. Today I set up IFTTT to check for starred Google Reader feed items, and automatically do everything else beyond this that I find annoying. Perfect!

IFTTT will check for custom recipe triggers every 15 minutes, so it isn’t something you’d want to use for actions you require to be instantaneous, but it’s perfect for situations like the above. The services with which it is integrated are many and varied, and the possibilities therefore nearly limitless.

UPDATE 16/04/2014: I just came across this page and found that I had referenced the now defunct Google Reader. When Reader died I moved all of my RSS feeds across to feedly, which IFTTT supports with identical functionality. I also apply the same rule to twitter posts I favourite, meaning that I have a Gmail folder in which IFTTT aggregates all of the stuff I want to read from both feedly and twitter.

Can the iPad2, with its 132ppi 1024 x 768 screen, be used to comfortably read pdfs without the need to zoom and scroll about single pages?

That was a question that troubled me when I was splashing out for one earlier this year. To try to get a better idea of what a pdf viewed on only 800,000 pixels might look like was hard. Neither my attempt to I resize a pdf window to the correct number of pixels (too small) nor my attempt to screengrab  a pdf at a higher resolution and shrink it using GIMP (too fuzzy) were particularly informative. I just had to take plunge and see.

There’s enough wiggle-room (as you can see in the screenshots below) to suggest that there’s no definitive answer, I think the answer is probably yes. But, that’s only if you take advantage of some nifty capabilities of pdf-reading apps, Goodreader being the one I use, mostly thanks to its almost seamless Dropbox syncing capabilities.

Below is a screengrab of a standard, US letter-size, pdf, displayed unmodified on the iPad. The size, when the image is viewed inline with this text (and not in its own separate window), is approximately the same as it appears on the iPad (there is some loss of resolution which can be recovered if you click on the image and open it in its own window).

Click on the image to simulate holding the iPad close to your face whilst squinting.

The screengrab above demonstrates that virgin pdfs aren’t great to read. The main body of the text can be read at a push, but it’s certainly not comfortable.

Thankfully, the bulk of the discomfort can be relieved using Goodreader’s cropping function, which allows whitespace around pdfs to be cropped out (with different settings for odd and even pages, if required).  A cropped version of the above page looks like this:
A marked improvement which could be cropped further if you weren't too worried about losing the header information. Click on the image to see the screengrab with no loss of resolution.

The image above demonstrates that cropping can be used to get most value from the rather miserly screen resolution (the same on both the iPad and iPad2, though almost certainly not on the iPad3, when that’s released).

But, cropping doesn’t solve all tiny text traumas.  There are some circumstances, such as with particularly small text like the figure legend below, that necessitate a bit of zooming.

The figure legend is a little too small to read comfortably, even when the page is cropped.

I don’t mind zooming in to see a figure properly, but that’s probably a matter of personal taste.

If you’re used to using an iPhone4, with its ridiculous 326ppi retina display, then you’ll find reading pdfs on a current model iPad a bit of a step back. But, it’s passable and I certainly don’t mind doing it. It certainly beats printing, carrying and storing reams of paper.

Having deleted my facebook account nearly two years ago, as I activated a Google+ account this week I was wary of repeating previous mistakes.  Back in 2009 I had decided that I wasn’t getting as much out of facebook as I was putting into it. Specifically, I was ashamed at the amount of my time it consumed, I was worried, not so much about my privacy, as the disregard of my right to it (even if I chose not to take it up), and I was anxious about expressing myself too freely lest I cause offence to my friends.  Google+ has lessened my anxiety with its subdivision of friends into circles, though, of course, its potential to cause me shame and worry over my time and privacy are just as real as they ever were with facebook.

With all this in mind, my early experiences of Google+ have been very positive. As I was hoping to, I have re-connected with some lovely friends who had remained on facebook and never ventured onto twitter. Perhaps most encouragingly though, it looks like Google+ might be able to reach beyond the social, and enrich my professional life too. The following exchange, which I started to try and learn more about the use of Amazon’s Mechanical Turk in psychological research, is the sort of thing that’s making me very excited about this possibility.

Full Google Plus conversation

The discussion went in to far more detail than I could have hoped, and for those who are interested, a text-searchable pdf of the exchange complete with clickable links is available here.  (Incidentally, the reason I have had to go to so much trouble to provide a link to the thread with jpgs and pdfs, as opposed to the sort of easy html permalinking offered by twitter, is down to Google’s as-yet imperfect post-hoc sharing system. Once I decided that the thread deserved a wider audience, the options available to me were a) to re-share my original post, without the comments, to anyone on the web, or b) to provide a permalink to the whole thread that was only accessible to those with whom I had originally shared my first post. An option to change the sharing permissions for the entire thread, with the permission of all contributors of course, would be highly appreciated!)

As to why the question about Mechanical Turk generated so much useful information, there are three reasons I can think of.  The first is a simple affordance of the length of posts and comments.  Unlike twitter, detail can be provided when detail is required.  Whilst I have read the thoughts of writers praising the cognitive workout required to condense their tweets to be both eloquent and informative, it is limited medium that doesn’t lend itself to information-rich content or detailed evaluation.  Google+provides a clean, long-format forum in which ideas can be effectively transferred.

The second reason lies in the flexibility of the medium to provide relevant information to those who care.  Circles can be used to selectively share updates with certain groups.  This means that scientific updates can be restricted to my ‘Science’ circle, posts on running can be restricted to my ‘Runners’ circle,  and users may be feeling the effects of a more targeted dose of updates and information.  Comments aren’t driven by a desire to appear funny to a large number of people who probably share your boredom at the fact that, as it’s Sunday, Akira has once again completed a 6.3 mile run in a smidgen over 50 minutes – you’d probably only reach 5 people who would actually be rather preoccupied with trying to work out why Akira hasn’t managed to improve on his 6-mile time despite having done the same run every week for about 6 months.  Depending on your willingness to invest time in the categorisation of contacts, you can be taken as seriously as you want.

Finally, and maybe most importantly, Google+ is current rife with early-adopters. These are technologically ‘switched-on’ folk, who are willing to take a punt on a new medium, testing its capabilities and its uses as they go. To illustrate, Tom Hartley, Tal Yarkoni and Yana Weinstein all maintain current blogs/websites of their own and all contributors to the above thread are active twitter users (and well worth following).  Asking a question about how to conduct science using a nascent technology via a nascent communication technology stood every chance of being successful given the overlap in the Venn diagram of technology users.  Add to that the diminished risk of being called out as a ‘geek’, we’re all geeks here even before uber-geeks are further isolated within the ‘Geek’ circle, and we have the optimum conditions in which to find out about Amazon’s Mechanical Turk.

This isn’t to say that Google+ won’t be successful for non-technological academic discussion, or for technological discussion even after the the laggards arrive.  But I think that success depends on the parameters for its use in academia being established now.  If academics recognise that Google+ can be used to exchange work-related ideas early on in its life-cycle, then it has a much better chance of taking off and even being further developed with this use in mind. It already seems to me a far more attractive site for academics than academia.edu which has comprehensively failed to do anything other than act as a repository for electronic papers and CVs.

So, I’m quietly optimistic… until the next big thing comes along and I jump ship, desperately trying to keep up with all the other early-adopters.

[youtube http://www.youtube.com/watch?v=suJgV9HhJp8]

Last night I capitulated and ordered an iPad2.

Since blogging about whether it might be a good idea to get one a while ago, I have noticed mention of iPads cropping up more and more in my RSS feeds.  Of course, this is down to the release of the latest version of the iPad, but I generally find it easy to ignore the engadget hype posts about stuff I’m not all that excited about… for example I really don’t give a toss about the Nintendo 3DS and there’s a fair amount been written about those lately too.  More difficult to ignore have been the mentions in the academic blogs I subscribe to (such as the consistently interesting Profhacker) and recommendations from friends (such as @pam_psych).

Other contributing factors have included the construction of  a ‘reading nook’ in my office, having to over-ride my HP printer’s helpful out of ink notification (if you’re out of ink, why can I override you and still get perfectly readable printouts?)  and noticing my ‘to read’ GMail label pile up to over 20 items once again.  The straw that broke the camel’s back was seeing Alex Easton give a very smoothly presented departmental seminar on Friday, all administered using, rather inevitably, an iPad.

Steve Jobs while introducing the iPad in San F...
Look at his smug little face. Image via Wikipedia

Which has led me to quite a conflicted state of being.  I dislike Steve Jobs immensely.  I despise the arrogance with which he suggests that the iPad is “magical” (I invariably had to stop myself from spitting on the sign that proclaimed this ridiculousness outside the Washington University Bookshop).  I even bought an Android phone so I wouldn’t line his pockets.  But the allure of a well-designed, perfectly useful product has made me eat my words and give him some of my heard-earned cash.

So, I’m now looking forward to the day in May when I receive my magical and revolutionary product.  I’m eagerly awaiting the sense of frustration I’ll feel when I realise that its 1024×768 resolution isn’t quite good enough to read a single page of a pdf article in fullscreen.  I can’t wait until the perfectly standard use of Flash on a website I’m viewing fails to load.  I’m on tenterhooks to experience the pointed glances that scream “pretentious wanker” at my smug little face.  Because from within my £399 walled garden, I will have even more reasons to dislike Mr Jobs.

 

Whilst Windows easily copies lots of data, it struggles when you ask it to copy lots and lots and lots of data.  Teracopy is a neat file copying utility that provides peace of mind as you transition from copying gigabytes of data to terabytes of data.

In order to get my fMRI data from St. Louis to St. Andrews, I have embarked upon the somewhat arduous task of copying everything to a portable hard-drive.   After a few attempts that ended in the failure to copy a file or two, seemingly at random, I lost faith in using the standard drag-and-drop copy in Windows, and searched for alternatives.  The command line option seemed fastest, but I didn’t want to bring the server down for everyone else for a few hours whilst I did my copying.  Then I found Teracopy.

A picture of TeraCopy
Teracopy in action (Image via Wikipedia)

Teracopy (freeware) is a straightforward utility that improves upon the Windows interface in a number of ways.  Copying is (apparently) faster and it certainly seems more reliable than the standard Windows approach.  One very nice feature is that it allows you to pause and resume your copying for when you need to free up system resources temporarily.

download Teracopy

So far I have copied close to a terabyte of data onto my portable hard-drive with no problems.  Now all that remains is to check it all with another utility (Windiff) to make sure all my files really did get copied successfully, and to actually transport my hard-drive without banging or dropping it.

fMRI scans produce an awful lot of data.  Depending on whether you’re getting you scanner to output 3D or 4D data, you can end up with one file per measurement, or file per scan.  If you’re dealing with 3D data (the one files per measurement option), you’re in for a long night if you decide that you don’t like the existing file-naming convention, and want to replace it with something a little simpler e.g. if you want to remove unique identifiers to allow for batch processing .  For example, the experiment I’m testing right now collects 292 measurements in each of its five functional scans, that’s 1460 files in total.  If it only takes me a three seconds to rename a file manually, then it’ll still take me over an hour to finish, and that’s just for one participant.

Of course, you could script something to do this pretty quickly, there’s an even easier way: Ant Renamer.

With a few clicks, you can select all the files within a folder (and its subfolders) and carry out a pretty versatile range of file renaming tasks in seconds – it takes about 5 seconds to rename 1460 files once I tell Ant Renamer what to do.  I use it to remove unique identifiers from fMRI data filenames, but the options are there to delete the first x characters from a file, change the extension, add incremental numbers to filenames, even use MP3 metadata to rename MP3s.

Ant Renamer is well worth investigating if you ever find yourself daunted by the prospect of file renaming in bulk – I’ve found it so useful that I keep a portable copy (no install required) on my dropbox so that I can access it on the move.