udden change in plans and improvement of research direction leads me to the exploration of MRI tagging, which proves to be difficult when one tries to actually find raw data to work with, not information about it. In the coming days I plan to prepare a post explaining to people where they can obtain tagged data of the brain and the heart (trying to help others solve the problem which occupies many hours of my time). The Internet is extremely mature when it comes to sharing of text and sometimes even audio and film, copyright being an obvious barrier. When it comes to medical data, however, it is another story altogether, even if it’s totally anonymised. Personally, I’ve put 3-D scans of my brain on this Web site, hoping to provide people with the sort of data I sometimes struggle to get a hold of.

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.
___
^* It was far, far uglier a few years back.

Back to nature… sort of…

London (2010)

arlier today I watched with great patience this wonderful new interview with PZ Myers (thanks, Thunderf00t!), who spoke about his hugely popular science blog. I very much enjoy his site in which he started writing only 7 years ago. It was about 6 years ago that I started my own science blog (on computer vision) and later started another one about my particular area of focus (that was in 2005). They grew nicely and reached the niche whose narrow topic of interest they covered.

I have been thinking recently of the potential to inform people who are my peers through scientific blogs and decided that I will probably restore activity in those older two, as well as this one neglected personal blog where I hardly wrote anything for the past 3 years (it totals 1416 posts though, mostly from the olden days).

I found it gratifying back in the days around 2006 when people in my scientific field knew me in conferences because of my blogs and wanted to hang out with me because of these. The readership grew steadily as long as I kept writing. PZ Myers sees the same type of trend and Techrights, where I wrote over 11,000 posts, is the same. Perhaps I will resume posting in blog form about science later this month or next month. As always, I will separate my professional life, my personal life, and my hobbies (the 4 blogs I run will provide this separation).

On several occasions I was offered an opportunity to write a book, but frankly, I believe that books are seeing their end of days (when older generations are no longer with us, then pen and paper too may vanish). I was fortunate to get into blogging early on, thanks to Free software. It’s a rewarding experience even through there is no pay.

ack in early 2008 I wrote about my transition into a more idle mode — a mode which enabled me to focus on some more personal projects and de-emphasise research for a while. Between the years 2003 and 2006 I spent a lot of time building and maintaining schestowitz.com to the point where it attracted about 3,000 visitors per day. In late 2006 I relocated a lot of my work and writings to the site now known as Techrights. This is where I publish a lot of my opinions and the fruits of my readings, which fortunately helps many other people understand the industry (no spin, no bias, no conflict of interest or money at stake).

I have been thinking about returning to research at a higher level of capacity than at present because it is something that I enjoy doing and something that keeps me abreast of my field of expertise. I will write at a later date about my plans.

Y intent is never to promote anything. I just try to find facts that are usually separate from consensus, which is very typically distorted, e.g. in politics (“war on terror”).

Some people are concerned about facts because we are all very skilled at beautifying our own integrity. The reporter who is selected to cover for a publication based on inclinations, convictions or obedience, for example, is often sufficiently indoctrinated so as to actually believe his/her writings, say X, about Y (well, “everyone else is writing X about Y too”). It’s a cyclic trap, it’s sheep/cattle effect. It’s a self-fulfilling prophecy in a sense. We see it in Comes exhibits (e.g. “The NC is dead” roadshow) and the Gartner Group was openly accused of doing the same thing to set standards.

Only by challenging conventions with facts can we find truth, then present it and preach to defend it (money always fights against truth).