Using Image Data

We at FIASCO Headquarters believe that it is always best to use raw k-space data, just as it comes off the scanner. Certain kinds of noise get frozen in when the data is reconstructed to make images. Since the goal is to remove as much noise as possible, working with the k-space data is preferable to working with reconstructed image data. However, FIASCO can deal with image data if necessary. It does so in part by transforming it back to k-space for the early stages of processing.

In analyzing image data you should always use the "FIASCO epi" command and files. Echo-planar imaging (epi) files use sample points in a rectangular grid, which corresponds to the sample grid in an image file.

Set the following four variables in the epi.local.csh file:

#space that data lives in: k=kspace  i=ispace
setenv F_READER_SPACE i
#EPI reordering of slices? 0=no
setenv F_READER_REORDER 0
#vector length 1=scalar 2=complex
setenv F_READER_VECLEN 1
#baseline reverse
setenv F_BASELINE_REVERSE none


F_READER_SPACE

Setting this variable to i tells the new reader script that the data is image data rather than k-space data.

F_READER_REORDER

Raw MRI scans do the slices in a strange order- all the even slices in a given image, then all the odds. These have to get reordered at some stage. Since your image-space data was reordered when it was originally reconstructed, you don't want FIASCO to reorder it again.

F_READER_VECLEN

K-space data is inherently complex, containing both real and imaginary components. When scans are reconstructed to produce images, the complex phase information is generally thrown away to leave only magnitude data. That is the point at which information gets lost. Since image data has only a magnitude (1 value) rather than real and imaginary parts (2 values), set this value to 1.

F_BASELINE_REVERSE

In EPI the lines of k-space are collected in a zig-zag pattern (scans across a line, drops down to the next, scans back across that line, repeated). So in reconstructing the images every other line needs to be reversed. Image data has obviously already had this done, so set this variable to "none".