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
