Doing the Analysis

Once the blood and image files are prepared, the analysis can be performed. Start MATLAB by typing matlab at the shell prompt. Starting the analysis is very straightforward. You may type help rcbf2 to get information on running the rCBF package. Basically, rcbf2 is a MATLAB function that returns a K₁, k₂, and V₀ image, as well as the delay found during blood delay correction. It requires the name of the MINC file that contains the images, and the number of the slice to analyze. Therefore, if we wished to analyze slice 12 of arnaud_20547.mnc, we would call rcbf2 as:

     [K1, k2, V0, delay] = rcbf2('arnaud_20547.mnc', 12);

In this case, the semi-colon at the end is very important since rcbf2 will return the entire images. If the semi-colon is omitted, the K₁, k₂, and V₀ values for every pixel will be echoed to the screen, which takes a considerable amount of time.

Once the images have been generated, they may be manipulated using any of the normal EMMA tools (viewed with viewimage, saved with putimages, etc.).