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8/21/2008
As anticipated, there has been little or no activity lately. However, I presented some of the latest development at Oxford last week. The presentation slides are finally online (in a variety of formats).
<ul>
<li><a href="/Research/Presentations/2006/MIAS-IRC-2006/final">HTML</a></li><li> <a href="/Research/Presentations/2006/MIAS-IRC-2006/MIAS-IRC_2006-final.pdf">PDF</a></li><li> <a href="/Research/Presentations/2006/MIAS-IRC-2006/MIAS-IRC_2006-final.swf">Flash/SWF</a></li><li> <a href="/Research/Presentations/2006/MIAS-IRC-2006/MIAS-IRC_2006-final.odp">OpenDocument Presentation</a></li><li> <a href="/Research/Presentations/2006/MIAS-IRC-2006/MIAS-IRC_2006-final.ppt">PowerPoint</a></li>
</ul>
Regarding progress, I handed in a draft of my thesis at the end of August. I am still waiting for feedback. more
[<em>This will be personal item rather than a technical one</em>]
am attending Medical Image Understanding and Analysis 2006, which begins later today. I will present my work tomorrow. There is also the possibility of a meeting at UCL next week -- one whose aim is to unify registration, modelling, and segmentation. It is part of a long on-going effort which occupies the entire inter-disciplinary research collaboration (IRC).
I write up my thesis nowadays, so it is unlikely that I will make any technical progress in the next few months. I will try to post technical items as soon as something interesting emerges. more
S of last night, a revised submission was sent to be considered for a special TMI issue on validation. This time, for a change, we included time estimates for ground-truth-free assessement on non-rigid registration in 3-D.
<br><br>
Concurrently, a related paper was accepted as an oral presentation in Medical Image Understanding and Analysis (MIUA) 2006. I will post a link to that paper as soon as I put it online. more
<br><em>An appearance model built from37 brains
<br>±2.5 standards deviations shown</em>
<b>UR assessment framework, which can either evaluate non-rigid registration (NRR) algorithms or evaluate models of shape and intensity (appearance models), has been extended to 3-D</b>. It requires <em>no</em> ground truth. Among other recent development, perhaps the most notable one is that which involves running some these algorithms the in 3-D to obtain encouraging, bug-free output. Due to the immense scale of this problem, true assessment of NRR in 3-D requires clusters, where the program can be easily deployed.
<br></br>
In other news, we are expecting to have our work included in an issue of IEEE Transactions in Medical Imaging. The initial reviews were very positive and we are running further experiments to alleviate any doubts. more
URTHER on the subject of <a href="http://schestowitz.com/MARS/modules.php?name=News&file=article&sid=24">entropy in registration and model assessment</a>, there is finally an intent to publish a paper -- one which explains it in greater level of detail. The process involves treating non-rigid registration (NRR) results merely as correspondence. This correspondence builds an appearance model, for which an entropy can be computed.
An entropy can be perceived as a measure of complexity as it corresponds to minimal message length that can <em>encapsulate</em> -- in this particular case -- a model of appearance. By computing such entropies, not only can the models be evaluated, but also the NRR algorithms from which these model were built. This essentially enables one to measure both NRR quality <em>and</em> model quality in an information-theoretic fashion. This method requires no ground-truth knowledge or manual annotation of any kind.<br><br> more
Our paper to <a href="http://www.biomedicalimaging.org/">ISBI 2006</a> has just been accepted and it is available on-line as well:
<ul>
<li><a href="/Research/Papers/2006/ISBI_2006/Final/isbi_2006.pdf">PDF</a></li>
<li><a href="/Research/Papers/2006/ISBI_2006/Final/HTML">HTML</a></li>
</ul>
<b>Abstract</b>:
E compare two methods for assessing the performance of groupwise non-rigid registration algorithms. One approach, which has been described previously, utilizes a measure of overlap between data labels. Our new approach exploits the fact that, given a set of non-rigidly registered images, a generative statistical appearance model can be constructed. We observe that the quality of the model depends on the quality of the registration, and can be evaluated by comparing synthetic images sampled from the model with the original image set. We derive indices of model specificity and generalisation that can be used to assess model/registration quality. We show that both approaches detect the loss of registration as a set of correctly registered MR images of the brain is progressively perturbed. We compare the sensitivities of the different methods and show that, as well as requiring no ground truth, our new specificity measure provides the most sensitive approach to detecting misregistration.
<br> more
<b>REVIOSULY we used model indices, which we called Generalisation and Specificity, to assess the quality of appearance models, as well as the quality of non-rigid registration</b>. We have now identified a valuable surrogate to these indices: Shannon's entropy. Some work by Hero <em>et al</em>. is encouraging the use of entropic measures to assess (dis-)similarity of graphs. This is practically used as non-rigid registration similarity measures -- somewhat reminiscent of mutual information (MI).
<br><br>
We intend to see if an entropic measure of clouds overlap suprasses the performance of Generalisation and Specificity. We also consider image distances that are based on K nearest neighbours (kNN) or the nearest match to a pixel intensity, a map of which is shown below. Since it takes around 20 minutes to generate each of the images below, we consider this to be highly impractical. To run just a single such model evaluation, we would need over 60,000 hours of computer power. And this is 2-D only...
<br><br>
Extension of our approach to 3-D is foreseen nonetheless. It will probably use the methods which require only a couple of hours of computation in 2-D. Resolution 'pyramiding' (coarse-to-fine approach) can assist in terms of speed.
<br>
<br>Top: original image; Bottom: nearest match to pixel of greyscale value 20, 60, 100 (left-to-right) for each of the other pixels in the image more
We shall be presenting our registration assessment work this Tuesday. A camera-ready version of the accompanying 2-page abstract is available on-line:
<ul>
<li><a href="/Research/Papers/2005/MIAS_IRC_2005/Final/manchester_mias-irc_final.pdf">PDF</a>
</li>
<li><a href="/Research/Papers/2005/MIAS_IRC_2005/Final/HTML">HTML</a>
</li>
</ul> more
E may soon start working in collaboration with the <a href="http://www-ipg.umds.ac.uk/mias/gridprojects/miasgrid.shtml">MIAS-Grid</a>, as well as the IRC. MIAS-Grid, where MIAS stands for Medical Images and Signals, is a project which ultimately produces an e-Science workbench for medical image analysis. To demonstrate the utility of the system, a series of use-cases is required and our code might be among these.
<br><br>
Essentially, the Grid might have our registration assessment algorithms re-created. It will then compartmentale the processes and carry out some analysis in a transparent way that has robust, well-understood interfaces (e.g. <a href="http://www.xmlrpc.com/">XML-RPC</a>). Subsequently, these processes can be embedded as workflows within the workbench, which might involve autonomous and powerful computers. Algorithms can easily be exchanged, thus enabling benchmarks (comparisons) to be rapidly conducted. The idea is reminiscent of the principles and rationale behind the Strategy Patten in OO programming.
<br><br>
<a href="/IMG/research/registration_benchmark_framework.png"></a><br>
Image registration assessment: the benchmark architecture<br>
Click image for full-sized version
<br><br>
We are not too certain about the future of this initiative and, in particular, some of the technicalities. Yet, we would feel privileged to have an opportunity to work on such modern computing architectures. Our particular set of binaries can directly benefit from parallel workflows. In short, here is the framework that can be envisioned already:
<ul>
<li>We are given a set of N images</li>
<li>We have M such image sets</li>
<li>We need to build a model for each set among these M sets. That can definitely be done in parallel and there is no apparent dependency</li>
<li>We now proceed to evaluating M models and again there are no dependencies among the evaluation processes</li>
</ul>
To add some context, <a href="http://www.schestowitz.com/MARS/modules.php?name=News&file=article&sid=16">registration is evaluated through the construction of appearance models</a>. All in all, the process in question need not be serial and it can be handled merely (not entirely) in parallel. We can further refine speeds by treating sub-sets of data (chunks) and then aggregating the results, if needed.
<br><br>
This would be similar to things we have done in the past, such as deploying banaries in computer clusters, invoking them via SSH, and collecting the output later. At extremity we used <a href="http://schestowitz.com/Weblog/archives/2005/02/25/a-necessary-hog/">30 units overnight</a> to produce some urgently needed results.
<br><br> more
HERE are some encouraging results (shown above), which show that we can evaluate face models quite reliably. We build <a href="http://schestowitz.com/Weblog/archives/2005/02/13/appearance-models/">appearance models</a> from a set of 68 facial images and control the quality of such models by distorting the effectiveness of manual markup. We then evaluate the models using a technique described previously in the <a href="http://schestowitz.com/MARS/modules.php?name=News&file=article&sid=19">context of MR brain datasets</a>.
More technical and comprehensibe reports on face models evaluation:
<ul>
<li>Evaluating Registration - <b>Draft</b> (<a href="/Research/Papers/2005/Evaluating_Registration_Draft/evaluating_registration.pdf">PDF</a>, <a href="/Research/Papers/2005/Evaluating_Registration_Draft/HTML">HTML</a>)</li>
<li>Generic Model Evaluation Method (<a href="/Research/Papers/2005/Generic_Model/generic_model_evaluation_method.pdf">PDF</a>)</li>
</ul> more
8/18/2008
8/13/2008
That is odd but non free video drivers might pull you down. Check out what Mark Shuttleworth had to say about binary blobs here. I’ve even had trouble with the free i810 drivers because it used bios routines that killed power management for me. That experiment lasted about five days before I ran back to 2D.
64 bit Lenny works well for me on my dual core AMD. I suspect this is because it minimizes the binary blobs and I’ve never installed anything from non free. If you use E16 and take advantage of their pagers you can do without multihead. If you need accelerated graphics, you could be out of luck for a year or two.
It’s been about five years since I compiled a kernel. It’s been easier and cheaper to replace things that don’t work with free software than it is to struggle with blobs from people who don’t wan to cooperate in the first place. more
7/25/2008
7/19/2008
America's economy is in utter ruins. And mostly because of Dubya's agenda of foreign invasion (trillions of dollars wasted). more
7/15/2008
Rambling around Zurich, Switzerland -- Photos by Lital Schestowitz more
The trip back from Zermatt to Zurich, 20/12/2004 -- Photos by Lital Schestowitz more
Pictures of the Matterhorn -- Photos by Lital Schestowitz more
Pictures around the village -- Photos by Lital Schestowitz more
The streets of Zermatt at night -- Photos by Lital Schestowitz more
Miscellaneous pictures from Zermatt -- Photos by Lital Schestowitz and <a href="http://www.schestowitz.com/Images/images4.htm#003" title="Gabriel Schestowitz">Gabriel Schestowitz</a> more
Lital on the Sunnegga -- Photos by <a href="http://schestowitz.com/roy" title="Roy Schestowitz">Roy Schestowitz</a> more
Pictures from Zermatt at daytime -- Photos by Lital Schestowitz more
Pictures from Zermatt at nighttime -- Photos by Lital Schestowitz and <a href="http://www.schestowitz.com/Images/images4.htm#003" title="Gabriel Schestowitz">Gabriel Schestowitz</a> more
Roy's messier room -- Photos by <a href="http://schestowitz.com/roy" title="Roy Schestowitz">Roy Schestowitz</a> more
Pictures of a gift -- Photos by <a href="http://schestowitz.com/roy" title="Roy Schestowitz">Roy Schestowitz</a> more
Various pictures from Zermatt -- Photos by Lital Schestowitz more
Rooms at the Zermatterhof -- Photos by Lital Schestowitz and <a href="http://schestowitz.com/roy" title="Roy Schestowitz">Roy Schestowitz</a> more
The dining room at the Zermatterhof -- Photos by Lital Schestowitz more
Pictures from the streets of Zermatt -- Photos by Lital Schestowitz more
Assorted photos from the astounding hills -- Photos by Lital Schestowitz more
View from the room -- Photos by Lital Schestowitz more
Dual-head, SuSE Linux, 2003-2005<br />
<b>Also see</b>: <a href="http://baine.smb.man.ac.uk:8001/screen.jpeg" title="Display Grab" rel="nofollow">current desktop screenshot</a> (<a href="http://baine.smb.man.ac.uk:8001/caption.txt" title="Capture time and details" rel="nofollow">Capture Time</a>, <a href="http://baine.smb.man.ac.uk:8001/archive" title="Daily archive of screenshots" rel="nofollow">daily archive</a>) more
Photos are low in resolution (<a href="http://schestowitz.com/Family_Photos/">Web cam</a>) more
7/13/2008
7/9/2008
7/7/2008
6/29/2008
6/4/2008
5/31/2008
Yes, Google helps FOSS in many ways, but it can become less responsive if its ego is deflated. I've noticed some Windows-only biases from them recently. more
"There’s life beyond Ubuntu, which I’ve occasionally used and still use since 2004/2005. Exploration is key, and it’s fun! Savour the choice."
Yes, there is, but you have to admit, it's the most usable (non-Microsoft-patent-agreement-mark-of-the-beast) and marketed distro. I've tried many and continue to try others but Ubuntu is the only one I roll out to others of all ages.
Regarding Google: "It’s a nice brand, but it typically just buys most of its software (other companies) and sticks it’s valuable labels on them. That’s not inspirational at all."
Not inspirational? It has a repo for Linux software, the positives you mentioned, and it has given us a lot of goodies for free. Sure, there's always marketing and advertisements around, and of course they're making money off of what they're giving to us but how many other companies like Google offer so much? I would argue that Google is an inspiration to us all, excluding censorship in China but Microsoft and Yahoo and other big names are also guilty of that.
Regarding Digg: Yes, it's a crap site now for the reasons you mentioned, but it was glorious watching you post there and fight the good FOSS fight, it got pretty crazy after awhile with people attacking you verbally and some even using your photo to mock you, which I thought was in very poor taste, but this is what Digg has become, it's like the MySpace of news sites, a bunch of vermin kids who know little about tech mixed with companies paying people to post and digg.
Keep up the excellent work with BoycottNovell.. looking forward to a #boycottnovell Freenode IRC channel. more
"There’s life beyond Ubuntu, which I’ve occasionally used and still use since 2004/2005. Exploration is key, and it’s fun! Savour the choice."
Yes, there is, but you have to admit, it's the most usable (non-Microsoft-patent-agreement-mark-of-the-beast) and marketed distro. I've tried many and continue to try others but Ubuntu is the only one I roll out to others of all ages.
Regarding Google: "It’s a nice brand, but it typically just buys most of its software (other companies) and sticks it’s valuable labels on them. That’s not inspirational at all."
Not inspirational? It has a repo for Linux software, the positives you mentioned, and it has given us a lot of goodies for free. Sure, there's always marketing and advertisements around, and of course they're making money off of what they're giving to us but how many other companies like Google offer so much? I would argue that Google is an inspiration to us all, excluding censorship in China but Microsoft and Yahoo and other big names are also guilty of that.
Regarding Digg: Yes, it's a crap site now for the reasons you mentioned, but it was glorious watching you post there and fight the good FOSS fight, it got pretty crazy after awhile with people attacking you verbally and some even using your photo to mock you, which I thought was in very poor taste, but this is what Digg has become, it's like the MySpace of news sites, a bunch of vermin kids who know little about tech mixed with companies paying people to post and digg.
Keep up the excellent work with BoycottNovell.. looking forward to a #boycottnovell Freenode IRC channel. more
2/22/2008
I friend sent me the following E-mail an hour ago:
<blockquote><b>time for a Digg fork?</b>
For some time now, a group of friends have been discussing the fact that Digg seems to be controlled by a professional astroturfers. Stories about Apple and Microsoft make the fp a lot, and FOSS less so.
Maybe we should respond by creating a separate service with a completely different URL that just mirrors the FOSS stories there, and stop going to digg itself. We could then have a place to go to read FOSS-related stories, without having to plough through all of the news about proprietary code that is not interesting to us. It would also be a good business model. And, coincidentally, the digg software is FOSS, AFAIK, and so is forkable. I think that FS daily uses it.
</blockquote>
I guess FSDaily is already out there, but it's a case of preaching to the converted or the choir and the audience is rather small (I know because I see the effects of front page stories there quite occasionally). more
The recent digg algorithm changes were an attempt at reversing this dumpster effect, where before you might be able to get 50 diggs in 24 hours and almost be guaranteed a front page, now I've seen hundreds of diggs on upcoming articles waiting for the "thought police" unseen and unsung moderators...
Honestly I'm surprised you aren't one of em. ;-) more
2/19/2008
I agree, Digg is at best a link farm. They offer nothing new for the surfer. It is full of webmaster's Digging their own articles to get traffic. With the proliferation of these scripts now on the market, sites like netscape have got it right in just using this type of service as an adjunct to their existing website. When the novelty disappears, so will the service. Hopefully, in the meantime, link farms like Digg and Stumble will disappear quickly unless they re-invent themselves. more
2/2/2008
WOW! congratulations on the award...once again, that took a lot of hard work and discipline to achieve. more
1/9/2008
It looks like those domains are not used and if I remember correctly the .cc domains were free some time ago. Not sure if they are still free.
Regards
Grez more
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