Stuck with VTK

It's getting a nightmare trying to compile programs which use VTK+ITK. Today I spent the entire day trying to learn how to use VTK for visualizing a dataset. After our meeting I learnt how ITKImage has functions that can convert a gipl image to a vtk structured point set (i think thats what they are called). There is also an .exe called "convert" that converts gipl to vtk format.

The next two days, I will be spending mostly at Glu.

Meeting with Prof. Daniel

It was a short meeting that we had today. We talked about how important it was for me to get the visualization done as quickly as possible. From there on we are planning to segment the images somehow first using some fundamental segmenting algorithms like Region growing. At some point we intend to be able to automatically get data for creating a Statistical shape model for the pulmonary drainage veins.

I also discussed my meeting with Dr. Tim Cootes at Oxford. After showing him the different drainage patterns, Cootes suggested that it would probably be a good idea to use more than just one shape model to describe a single pattern. However, I also explained to him how difficult it was to acquire images for patterns which are rare.

After discussing the rarity of the patterns, Prof. Daniel suggested that it would probably be a good idea if we could create models for the rare patterns with whatever data we have, and then declare that the model has some limitations. He also said that we could find out what proportion (e.g. 95%) of the data it explains (not clear on this)

non PhD: How do you export highlighted syntax source files

Someone was asking me how you export a highlighted-syntaxed file to a word document. This is something I have never thought of in all the years I have programmed and created reports. Anyways, there is a solution. It happens that one of the editors out there has an export function that enables you to export its highlighted content to various formats such as PDF, RTF (works in Word), XML, etc.

The editor's called SciTE and here's the link to their page.

Subtraction works

I finally was able to subtract a Post Angio image from a Pre Angio image. The images are MRIs showing the pulmonary vessels. Subtraction, although a very trivial procedure, took me some time to figure out since I was new to the IDE.

The subtracted iamge reveals the blood vessels. Daniel has suggested that I perform a MIP (Maximum Intensity Projection) rendering on the vessels to analyze the structure. MIP can be easily implemented using the VTK library. I am doing some background reading on basic Computer graphics concepts such as volume/surface rendering. I have got hold of some papers and a book on the VTK library.

Installing Daniel's ITK

I have been trying since weekend (25th March) to set up Daniel's ITK. It has really been difficult. Thanks to Raj. He helped me a lot to set up ITK on Visual .NET. Sometime I need to sit down and write all the installation procedures.

It's simple, first you need to checkout the code (which vip calls Project) from CVS. I have been using Tortoise CVS on windows. You then need CMake to install the binaries, this step is important as CMake produces code optimized for your compiler. Next, it's just a matter of opening up the solution workspace on Visual .NET and building the solution.

What got me the most was how we are supposed to deploy code that we write, which uses the ITK. So for example, if we write code which uses the ITK library, our file (.cc) needs to sit under project/applications. CMake needs to install the binaries once again, and the solution needs to re-built. Its a nuisance doing it over and over again, but thanks to the Visual .net IDE which only compiles files which got recently changed. Look for an option which only builds the file and not the entire solution.

Oxford Uni. for Spring school

I spent a week (Mar 19- 24) at Oxford attending lectures given by some prominent researchers in the field of medical imaging. It was a great learning experience, and I enjoyed my time greatly. For any one interested in the Oxford Spring school, here's the link to their webpage.

The entire conference costs around 500 pounds, and the accomodation is included. We were given accomodation at St. Anne's College. It is a good idea to take your laptop with you. I survived the whole one week without a computer.

I met some people there who are also new researchers in the field of medical imaging. Notably, Arif Asif Qazi at the IT university of Denmark, and others. It was funny that I met a few people from Imperial College for the first time there. Ioannis (neurologist) and Mustafa Anjari (medic) are both working at the Hammersmith hospital, which is also a part of Imperial College.