Hi all,
I have a question about prescribing gradient directions to FDT.
Searching the mailing list I reckon that many posts concern this question,
but I cannot really figure out what to apply on my question.
We have acquired a DTI set on a GE scanner (v.12) with 45 directions and 6
b0. The slices were axial slices with the Frequency Echo (FE) in R/L and
Phase Echo (PE) in A/P (as defined on the scanner). For FDT I define a bvecs
based on the tensor.dat file used for feeding the gradient directions into
the GE-scanner (or actually I have a user-specified file with Jones
directions).
When running DTIfit then I get a V1-vectorfield which seems to be flipped
R/L. (e.g. wrong principal directions on axial images in Corpus Callosum or
coronal images in Internal Capsule). The FA-maps appears to be correct, as
one would expect if there is just a R/L problem.
I tried to flip the x-row in bvecs (x->-x), and then the fibers were correct
in the Corpus Callosum and the Internal Capsule. However, I am not certain
of what this problem-solving flipping means in practise...? So my question
is whether my images are defined incorrectly, whether I am feeding them with
non-congruant directions or whether the images and the bvecs (as they are
now) are just incompatible (e.g. defined in different spaces)? Or if
something else is wrong...?
I do the conversion of dicom->nifti with spm5 ("dicom import"), and this
seems to work fine as for all the avworient-stuff (radiological, sform/qform
are scanner anat with LAS). I read somewhere on the web that the gradient
directions on a GE-scanner are relative to FE, PE and SS-axis. Is this true?
What if I use oblique slices or have a set for which FE/PE/SS does not
correspond to x/y/z? How should I convert a gradient set into a bvecs file
so that FSL can interpret them correctly for these cases?
Thanks,
Finn Lennartsson
