These files each consist of data representing 156 1mm slices, 256x256, 2 bytes per pixel.
This is a lower res anatomic data file, 22 slices, 256x256x2, 5mm thick slices that exactly match the locations of the diffusion images. (Jim notes: - well, ALMOST match. Since I acquired 20 diffusion images (10 in difflow and 10 in difftop) I matched them to the center 20 anatomical images. So the very top anatomical image, and the very bottom one, have no corresponding diffusion image.)
This is the matlab code for veiwing the anatomic data as a slideshow.
This is the matlab code for the diffusion processing Jim does. The field map is actually created by other code, but this program shows how the field map (the displace file) is used to correct the diffusion images.
The field map. It has an odd size, 132x68, 22 slices, 2 bytes per pixel. It is raw data. This is the size the scanner acquires for this sequence (other sequences do 128x128, and other combinations).
A file related to the field map "displace" file. It is a measure of the slope of the field map in the phase encoding direction at each pixel.
These are the raw data files from the scanner. To make them easier to read, I have included a copy of the matlab code Jim uses to calculate the diffusion images, called bip3.m. These files have complex data, 4 bytes real, 4 bytes imaginary, per pixel. Matrix is 90x84. Header info is 8 bytes at the front end, and 68 bytes before each burst of data, which is 90x84x8 bytes long. There are 71 "frames", where each frame is all ten slices. After the first dummy frame, which is used to set the relaxation, Jim acquired 10 frames for each setting of the gradients.
The frames/gradients key is:
Frame Diffusion gradients
1 None
2-11 None
12-21 y
22-31 x
32-41 z
42-51 y and z
52-61 x and z
62-71 x and y
These are the diffusion images Jim calculated using bip3.m difftop.aniso is the anisotropy image, Bx and By are the diffusion weighted images with the diffusion gradient in the x and y directions, respectively. The ref image is an image acquired with no diffusion gradients. difflow is 10 slices that are just below the 10 slices in difftop.