Progress Report

Tuesday, November 30th, 2010

Progress and Agenda - Overview of Possibilities

Experiments - Recapitulation


MATLAB vs QtOctave

In KDE (Qt), despite MATLAB putting a lot of effort into improving the GUI on the GNU/Linux side, QtOctave integrates more nicely with the desktop. Some other tools of use include R, Sage, Scilab, QtOctave, and graphviz.

Framework - Ctd.

I test to see that code always works in both Octave and MATLAB. The syntax is compatible.

Octave sombrero

Framework - Ctd.

I'm also exploring the GPLv3-licensed BioSig project, which allows me to deal with DICOM datasets of the heart.

Octave packages Octave packages - window

Framework - Ctd.

DICOM is considered "extensible", which implies that the usual type of format incompatibility will always occur. It's just an inconsistent data format.

Here is the command-line converter that I use (some are for Windows only) 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.

DICOM in Octave DICOM in viewer

Tagged Data

Tagged heart

MRI tagging commonly used, not simple to find on the Web

Tagged Data - Ctd.

Tagging of heart

Based on the excellent Web page of Zhen Qian I have managed to piece together something for people to play with. From his thesis [PDF] I've extracted a series of 6 frames that I've produced the above videos from.


Tagging in the context of image acquisition involves getting magnetic signal by selectively sending charges to the tissue, whose atoms (usually just hydrogen is targeted by adjustment of frequencies) equipment can try to test for response in such a way that under normal conditions without noticeable change they would return a rectangular grid overlaid on top of the data. This enables better tracking of tissue motion that's robust to spatially-similar atoms (whose returned signal is hard to discern visually).

Real data example

Octave tagging

Synthetic data example

Octave tagging - synthetic

Future Directions