T HAS been a while since I last did a comprehensive survey of DICOM-related software and since I am ditching MATLAB (in the quest for Free software-only research) I decided to review or at least check out what’s available at the end of 2010. Other people may find this handy.

DICOM is notorious for being the standard that’s not quite the standard and is actually somewhat proprietary and controlled by one entity. As someone pointed out the other day, DICOM is considered “extensible”, which implies that the usual type of format ‘bastardisation’ will always occur. It’s just an inconsistent data format as someone warned, so some software would cough at it and sometimes manage to salvage some data. According to Wikipedia, some tagging of the image/s is accompanied by data fields like:

Let us say that we are more interested in the raw image data and not so much in the metadata. If that’s the case, batch conversion to a more manageable format is worthwhile. Here is the command-line converter that I use (some are for Windows only and they are proprietary) and some other options can be found on the Web through directories. There are also good software resources on scientific data formats and there is radiology CEU information regarding PACS and DICOM viewers. There is actually far more choice out there than there was a few years ago. For GNU/Linux and Free software proponents there is no lack or deficiency, either.

HIS POST is part of a series that I do about my incursions moving from MATLAB to Octave, which has so far been a pleasant experience. QtOctave looks better and is easier to install than MATLAB (on GNU/Linux with KDE at least). For those who experienced being a customer/user of MATLAB, it can really be a pain in the butt, licence-wise. The parent company, MathWorks, can be very aggressive when it comes to licensing (it pays the BSA after all), so people are kept tied to particular IP addresses and must renew something to remove artificial limitations. Moreover, the toolboxes that MATLAB sells separately are a case of artificial scarcity and they can be expensive. Octave resolves much of this by centralising a lot of software as shown in the screenshots above (also separating free/libre from proprietary). Rather than waste time with paperwork and bank transactions, any QtOctave user can simply and quickly click away to receive anything s/he desires. It’s truly like a candy store.

Why ever go through the trouble presented by MATLAB, Maple, Mathematica, or IDL? Some people may need these for collaboration and consistency (as in monoculture), but it is better to start without any proprietary software dependency.

I will report on more aspects of this comparison as I go along. At the moment I’m exploring the GPLv3-licensed BioSig project, which allows me to deal with DICOM datasets of the heart (images acquired just recently — ones that I picked up at the hospital yesterday). Speaking of which, I’ve learned that some scanning machines that traditionally used Windows are now moving to GNU/Linux. How exciting times are coming…

N A KDE (Qt) desktop like mine, despite MATLAB putting a lot of effort into improving the GUI on the GNU/Linux side^* (even adding a Microsoft Windows-esque “Start” button at the bottom left), QtOctave integrates more nicely with the desktop. Thanks to all those who suggested some other tools including R, Sage, Scilab, QtOctave, graphviz and so on as I make my way into the world of Free software-only research (valuable pointers in the comments too).

All the code I’ve ever produced is Free software, but whenever I worked with MATLAB only the underlying framework was proprietary. This created a sort of trap, wherein my free/libre code depended on code which was not. In the near future I hope to produce code, blog items, upload of all code I write (including code sample for explanatory purposes), screecasts, etc. I may even commit code upstream if it’s polished enough for general-purpose use. I will continue to share dents and images on a regular basis too. In the mean time, for comparative purposes, I will also use my academic licence of MATLAB. I was once ranked first in the world for my code contributions to MATLAB, but although my code was all free software it helped MATLAB (BSA sponsor and thus a contributor to an attack on the software industry) just sell more copies of proprietary software. I am not a disgruntled prominent user of MALTAB but someone who is trying to show the way out of MATLAB mostly for idealogical reasons. If everything works as I hope, I will soon be 100% free of proprietary software.
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^* It was far, far uglier a few years back.

It was interesting to find out why Ian had left to join Sun.

ERE are some thought about things I’ve observed in the past week.

Linux and Free Software FUD on the Rise in 2008

The attacks on OSS and Linux have ballooned since the new year began (LANCOR, Jeff Gould, McAfee and the ilk). I decided to just concentrate on squashing FUD and attacks. Please E-mail me (roy at schestowitz dot com) if you see something I have not covered somewhere on the Web. It’s something which must be addressed.

Be aware that Intel systematically spread FUD and sabotaged the OLPC project from the very start. The press never covered this properly. WSJ said that Intel staff also spread FUD in Peru. They were saying OLPC adapters should not work (a lie). Folks are encouraged to embargo Intel not only for this, but for its kickbacks as well. For two years, Intel has behaved like an appalling abusive monopoly, but the press did not cover the issues at hand. It looked the other way instead. When it comes to OLPC, Intel spread FUD. tried to gag Nick Negroponte with a ‘deal’ and also ‘competed’ by selling Classmate at a loss. Those who want to know the real story should start here.

Open Source in the United Kingdom

BECTA is responsible for the procurement of software in Britain’s educational sector, but its seems like a lost case based on what I’ve read. Such dinosaurs are dependent on the existence of software with acquisition costs attached. There are other issues however, including the danger of rocking the status quo boat.

Procurement is a matter of gut feeling or relationships. Pressuring those responsible by exposing them might be the most effective way to combat this habit. It seems to have worked out with the BBC, which gradually surrenders to pressure to stop its Windows-only affairs. One can find Mark Taylor’s piece in Groklaw (and Highfield’s hurried response to it). This shows how putting one’s job in jeopardy (for possible corruption) can lead to results.

GPL Lawsuits FUD

Some recent headline suggested the GPL is attacking, rather than being attacked (dishonoured). That was a fortnight ago. There is a lot of FUD at the moment in general. As pointed out above, McAfee brings back its 2006 FUD and attacks the GPL again.

Of course, McAfee relies on insecure systems to sell its products. It was caught spreading Linux FUD back in 2006 when it accused Linux of security problems. Fortunately, as a Linux user, I don’t even need to avoid McAfee products. McAfee are irrelevant to me. That’s why they are so afraid (defensive).

Where is the Old Open Source and What Did You Do to the Real One?

As the meaning of “open source” got so diluted and the business models of some new adopters assimilated to that of proprietary software, it become more apparent that Free software (as in GPL and its derivatives) was the way to go. That’s why GNU/Linux is so far ahead of open source in the enterprise when it comes to adoption.

In short, open source is something else whose value was radically warped. We have to ask ourselves if OSI-approved ‘open source’ means what it used to mean. If not, we’re killing the term and harm everyone who is honest, e.g. Digium, Red Hat, even MySQL. People ought to return to the term “Free software” and just emphasize that it’s about freedom. ‘Open source’ should have been more stubborn and selective. Have I lost hope in ‘open source’ because of the charts? No, that was months ago when I saw the thing devolving and called it quits.

Remember never to mix the penetration rates of open source with Free software such as GNU/Linux.