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:
The meanings of the variables are:
#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
setenv F_BASELINE_REVERSE none
- Setting this variable to i tells the new
reader script that the data is image data rather than k-space data.
- 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.
- 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.
- 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".