Thursday, April 1, 2010

My First Code

When I graduated from Physics department, I had no idea about programming. After I was accepted to Master program in Biomedical Engineering, I realized that I should have learned Matlab for course projects and thesis.
My first code just contained about 60-70 lines and it took me 1.5 months to complete! It was taking two types of images of the cells and calculating the direction of the motion for each cell on the images.
After this project, I became very curious about programming. I improved my Matlab knowledge and I began to study c++ and GUI desing.

Friday, March 26, 2010

Extended version of griddata3

The time consuming part of griddata3 function is delaunay tessellation. If there are multiple volumes having the same scattered coordinates, griddata3ev (ev: extended version) func makes tessellation once and apply it to all volumes.
If the volumes are too large, griddata3ev function gives memory error as griddata3 does. To get rid of such errors, griddata3evs can be used. It divides the whole volume to sub volumes, apply each of them griddata3ev, saves the results then merges them.
Here is the link: download

Fiber tracking

I used DTI and fiber tracking code to track fibers in DTI images of muscles. I optimized this code so that it can be faster for small region of interests.
The new version is here: download

Transformation matrix between two dicom image coordinates

This code is used to calculate transformation matrix between two dicom image sets acquired from an MR scanner using dicom info. Keep in mind that these two image sets should be taken with the same localizer and there should be no motion artifact.
The code first finds the transformation matrix between the two image coordinates and patient coordinate separately. With these two transformation matrices, you can match any point in two image sets.
I used it for TurboFlash and EPI DTI image sets.
Here is the link to Matlab codes: download

Tuesday, March 23, 2010

I am here, too

My name is Alper. This is my first entry to my blog. I would like to write about biomedical engineering, MRI, image processing and programming.