We had an fMRI paper accepted to the Journal of Cognitive Neuroscience earlier this week. Having got the science out the door, I was able to turn my attention to the fun stuff – a cover image. The cover image for my first fMRI publication was selected by the Journal of Neuroscience and I wanted to go with something similar.

In the past 6 months or so, @alby has tweeted some of the images he generated using @lowpolybot, a twitter bot that returns low-polygon renderings of images tweeted to it. I tweeted a figure from the accepted paper to @lowpolybot and got this back:

@lowpolybot image from the tweet: https://twitter.com/Lowpolybot/status/572392951634108416
@lowpolybot image from the tweet: https://twitter.com/Lowpolybot/status/572392951634108416

There are a range of operations @lowpolybot can perform on your images (detailed on the @lowpolybot tumblr), but if you give no instructions you will get a random combination of operations applied to your image. This was what I had done. I was happy with the picture so, having checked with @lowpolybot’s creator @quasimondo that he was happy for me to do this, I submitted it to the journal.

Sadly though, there’s no chance this image will b e used as a cover image. I received an email the next day from a journal administrator informing me that they have stopped printing cover images. Ah well.

 

I’ve been enjoying the views from my North Sydney apartment since I moved in. The view is incredible.

 

This morning, a couple of lorikeets landed on my balcony railing. These birds’ colours are incredible. I grabbed the ipad and snapped a few pictures through the window.

They seemed pretty curious, so I plucked up the courage to open the door and try and snap a few close-ups

They didn’t fly away, so I grabbed the first bird-appropriate food that came to hand.

A moment I will treasure.

 

Below are some quick-and-dirty brain outline images I’m using in a talk I’m giving in a couple of weeks. I like the calligraphic quality that the axial and sagittal slices have. The coronal image is a little more colouring-book in its outline.

axial outline
sagittal outline
coronal outline

They’re very easily generated with screengrabs from MRIcron that are processed in GIMP with a straightforward series of the following steps:

1) Edge-detect
2) Invert Colours
3) Gaussian Blur
4) Brightness-Contrast

Repeating steps 3 and 4 a couple of times will get the consistency of line seen in the coronal image.

Whole brain masks are produced by SPM when estimating a model.  They’re great to look over if you want to check  the extent of participant movement (a quick heuristic is to examine whether movement has been so severe that it has noticeably chopped off bits of the brain, e.g. the cerebellum).

These masks can also be used as large, whole-brain ROIs from which to extract signal to covary out of resting connectivity analyses.  I’ll write more about conducting resting connectivity analyses using SPM, without the need for a dedicated connectivity toolbox, at a later date, but it involves extracting timecourses from the whole brain, white matter, CSF and entering these as nuisance regressors alongside movement paramters and their first derivatives.  I use Marsbar to extract the timecourses from the ROI files saved in the *roi.mat format.

Recently, when combining a few different datasets into one bank of resting connectivity data, I noticed that the whole brain mask aggregated across the large number of participants was dropping out a lot of the brain – not enough to consider excluding individual participants, but cumulatively quite deleterious for the overall mask.  I therefore used Imcalc to generate a binary-thresholded image (thresholded at 0.2) of the SPM-bumdled EPI template.  As you can see below, once you remove the eyeballs, this makes for a nice whole-brain mask.

whole-brain mask image
Whole-brain mask constructed from SPM EPI template

I’ve zipped this mask and made available in roi.mat and .nii format here.

Every now and again, Microsoft Powerpoint or Excel graphs or illustrations turn out just as you want them. In these situations, it’s handy to have a way of saving each slide as a high-quality image file.  I’ve used the one-off registry tweak described below to successfully generate figures for journal articles from Powerpoint slides.

I used to do this by starting the Powerpoint show in fullscreen (having pasted the Excel graph into a slide, if necessary) and pressing Print-Screen (PrtScn) and pasting the screen-grab-quality image into GIMP to edit and save. This is perfect if the image you need only needs to be high enough quality to display on screen e.g. if you’re making instruction screens for experiments and don’t fancy messing about with coding each block of text for the instructions in E-Prime, Superlab, Matlab etc. However, if you need to produce files that you can submit to journals as figures, then you need something that’s much higher quality (usually journals will stipulate a minimum resolution of 300dpi).

The standard “Save As” .bmp, .tif, .jpg options in Powerpoint will produce some decidedly jagged, 96dpi images, which aren’t much good for anything other than making thumbnails of your slides. However, these is a tweak in the form of a Microsoft-suggested registry edit that fixes this and allows you to saves images with resolutions in excess of 300dpi.

http://support.microsoft.com/default.aspx?scid=kb;en-us;827745&Product=ppt2003

If  you follow the instructions, you’ll be able to set resolutions of up to 307dpi in Powerpoint 2003.

96_307dpi_images
96dpi image (left) and 307dpi image (right)

The images you see here are examples created from a 1″ x 1″ Powerpoint slide that I have enlarged (96dpi) and shrunk (307dpi) so they are comparable on the same scale.  You can see the fuzziness of the Powerpoint default output image on the left compared to the one on the product of the registry-tweaked image on the right.

WARNING: Don’t try and set the resolution to be any higher than 307dpi (on Powerpoint 2003) though, as if you do so and manage to avoid causing a crash every time you try and save presentations, on large images you’ll end up with images where the bottom-half looks like it has been squished up, leaving the text isolated – worse than standard 96dpi images as far as reader-comprehension goes!

This week, as well as being published in the Journal of Neuroscience (see here), our article-related artwork was also chosen to go on the cover of the journal.

JoN Cover - Brain Mosaic
The Journal of Neuroscience - Feb 24, 2010

When I was trying to think of something we could submit as a cover, I initially thought of trying to create a photo-mosaic of our key activation using the raw, mosaic images from the scanner.  That didn’t work out so well, largely because there is very little that differentiates one image from another amongst the thousands of mosaics that are gathered over the course of a single scan – they’re all grey, fuzzy and extremely boring to look at.  So, I tried it using renderings of the key activation viewed from different angles, and rendered in slightly different shades of red/orange/yellow, and it didn’t look too bad at all.

In order to do this, I used Steffen Schirmer’s Photo-Mosaik-Edda software.  It’s a wonderful program that’s pretty easy to use and extremely customisable and I was pleasantly surprised to find out that I could produce very high quality images (e.g. suitable for printing as a magazine cover) using the built-in settings.  I simply built a library of images which would act as the tiles of the mosaic and, then selected the image that I wanted the mosaic to represent.  In order to create the tiles, I used the indispensable MRIcron by Chris Rorden, and to get the size and layout of the larger image that I wanted, I simply messed about with one of the images in GIMP (I also relied heavily on both of these pieces of software to make the figures in the manuscript itself presentable).

I’m keen on the image because I hope it still captures some of the essence of what I was trying to get at – that in fMRI research we use tonnes and tonnes of data to create the pretty pictures that make it all intelligible.  Admittedly, it is pretty hard to make out the text on the cover of the Journal, but I’m glad that whoever saw fit to use the image was happy to take a hit on that front in order to use the image.