Resuming updates

There’s been a long, long gap since I posted significant updates. It all started when I decided I really need to improve the text emails I’ve been sending out to subscribers of version updates. Right now I have them link to their account centre in the website, which then links them to the programs they’re following. It’s not very 21st century. The new emails (not quite done) list each program separately, with a screen cap if appropriate.

This meant changing the emails from text to HTML, which is not entirely straightforward. There are quite a few ways to create an HTML email and include or link to images in various encodings, and I didn’t know any of them. Most software that’s available to help with this caters to the usual situation of sending the same email, or at least template, to a number of people. My emails are different for each recipient, and I create them from scratch, so I had to write software to write the emails, send them, track that they are responded to, and archive a copy on the web site.

This in turn led to another issue: the links to the program pages were horrible, long and insecure CGI URLs. I learned more than I ever wanted to learn about URL rewriting using .htaccess files, but it’s done, and programs now have a sensible URL like So I can include those into the emails, and it also looks much nicer in the browser address bar.

Months passed while I learned about and implemented these major features, and I had to put them aside to prepare for the Turku PET Symposium, a conference held every three years at the University of Turku in Finland. They very kindly invited me to give a talk on free medical imaging software, and I put a lot of time into preparing what I hope was an interesting 30-minute talk. The symposium was a great success and people said nice things about my talks, so I was happy. After the symposium I took five days to travel up to Lapland by sleeper train, just to see it. Lapland is a beautiful place and the people there are very special. Anyway that all finished last week and I am eager to get back to work and implement some of the plans I have for the site. Plus, list all the latest updates and evaluate and add the 30 programs that are waiting to be added.

Hago Imagen

Spain has been on the ascendant in 2010 and continues that dominance with two terrific new programs added to this site, both very advanced and from academic centres in Spain.

The first is SATURN, an advanced visualization program for Diffusion Tensor Imaging (DTI), which comes from Ruben Cardenes and colleagues at the Image Processing Laboratory of the University of Valladolid.  This program is an excellent example of cross-platform development, in this case using the ‘Fast Light Toolkit’ FLTK.  I downloaded and ran the Mac, Windows and Linux versions of SATURN and they look and run identically.  It’s great to see the program released on all three platforms with the same version.

DTI employs data sets storing tensor data, represented by volumes of multidimensional data.  As such, the program uses fundamentally different data file formats than those used by most other imaging modalities, which store one scalar value per point.  SATURN stores tensor data in VTK and NRRD formats, the latter is new to me, it’s a library and file format for storing multidimensional raster data.  The MR data is loaded from regular data, and the higher level abstractions of model data, or fiber tracts, are stored in the VTK format.

I can’t claim to have tested this program extensively since I’m unfamiliar with the modality (I must now try to drop the terms ‘fractional anisotropy’ and ‘mean diffusivity’ into conversations), but I did open the sample data sets and have a run through the menus.  This is a major, solid scientific application and a significant addition to this active and growing field.

I know little about DTI but I have seen an increase recently in the amount of software coming out in this field.  I’ve been wondering whether to classify it as a specialization of MRI, or a modality in its own right, and have decided on the former.  There are several other sub-fields of MRI (FMRI, DSI), and it seems more likely to come, and I don’t want to fragment the categories too much.  Also, programs such as SATURN can read ‘scalar’ or regular MRIs in DICOM format just fine, so it seems it belongs under MRI.  And anyone in this highly advanced and specialized field is going to be an expert, and will know where to look for the right software.  I don’t think it’s quite got to the point where they send you home with your DTI images on a CD.

Continuing the Spanish theme, the other program added is GIMIAS, from Xavier Planes and colleagues at the Universitat Pompeu Fabra, in Barcelona.  GIMIAS is a large and comprehensive dataflow-based environment for prototyping processing in medical imaging and several other disciplines.  That’s a broad description and this framework, accordingly, covers a wide swath and requires some study before use.  This is an application for the heavy tasks, and yet as installed, is easy to use for the most common imaging tasks: you can use it to view images and I also tested query/retrieve from my DCM4CHEE PACS server.  There is also the ability to save in various formats, and many advanced imaging features including volume rendering, segmentation, ROI definition and statistics, volumetric meshes and many others, detailed in the 84-page manual and large website that includes tutorials and demonstration videos.

The real power of the GIMIAS framework, though, is enabled by its workflow capabilities.  A workflow (several are included) is defined by the user as a series of processing steps, as shown her in the AngioMorphology clinical workflow.

Each step can be anything from loading the images, to image processing, to a complex process involving the user.  The workflow is defined using a drag-and-drop editor and of course can be saved and new workflows can be downloaded.

And if that’s not enough, the framework is fully extensible through a plugin architecture and a comprehensive API; source code is also available to download.  GIMIAS makes good use of existing free software including several popular toolkits used by other programs on this site: ITK, VTK, DCMTK and MITK.  Each one of these is a leader in its field: used well, as here, in a major project from a top academic lab, and great things result.

Firefox Rules!


mozilla.jpgBy which of course I mean, it rules the ratings.  Though it could also be said to rule, because it is a really good browser and was the first real alternative to Internet Explorer, back in the days when it was called Mozilla.  I kind of miss the old logo and the spirit of rebelliousness that came with not running Internet Explorer back in those heady days.  Though if we’re going to talk old web browsers I could hark back to 1993 and getting NCSA Mosaic for the first time…but I digress.

report_browser.pngSo, these ratings.  Here at I Do Imaging World HQ we (I) analyze the web logs on a regular schedule – given that I’ve done it twice,that is hard to disprove.  And when I looked at the web browser statistics I see that some time around July, Firefox because the most popular web browser used to access this site.  Of course, I credit my readers with being high achieving trend setters, so I don’t know if this reflects the web use as a whole.  Still, I think it’s a significant point in Web history.  Over the last two years, Internet Explorer has gone from almost 60% to just under 40% share, while Firefox has climbed from about 35% to just over 40%.  Safari and Opera have seen modest gains, from about 5% to about 8% each, with Chrome, which of course didn’t exist two years ago, now at about the same level.

Any one of these is a perfectly good browser.  In the last year I’ve been using Internet Explorer occasionally and have found that the latest release is actually really good.  I’ve been using Firefox for so long that IE has caught up a lot.  I use all five of these on the PC, on the Mac I use Safari, Firefox and Opera, and on Linux I run Firefox and Opera.  I really like Opera, partly for their adherence to standards (though all browsers these days are pretty good about that), but also I like to stick up for the little guy.  And, I can’t shake the idea that any software from Scandinavia is just plain cool.

report_os.pngOn the operating system side, things are a little less dramatic.  Most people still run Windows, though in two years this share has fallen from almost 90% to just over 80%.  The Mac has seen a steady rise, growing 50% in share from about 8% to about 12%.  Linux trucks along on the desktops of about 7% or so of the desktops of my readers.  For years and years I was among those hard-core souls, using a Solaris or Fedora machine as my primary workstation, but recently I’ve found little reason to use any machine other than my Mac Pro.  I still use it as a Unix workstation at the command line, but as far as my web stats are concerned, hello, I’m a Mac.