Hello Matthew,

in my experience, once you have the nii you're one step too forward to retrieve the bval/bvec files... These information are usually provided by the scanner technician, or are encapsulated in the raw images which come out from the scanner (e.g. PAR/REC files for Philips, and in general in the raw dicom files). So you must be able to aske them either to your technician, or to ask her/him the raw images. One simple way to get those information in a format which is already suitable to feed into dtifit is by converting the raw images into nii using the utilities provided with MRIcroN (dcm2nii and dcm2nii_gui).

In summary, as far as I know there is no way to retrieve the gradient orientation from the nii file, you must be able to go back to the raw images or to get the acquisition scheme from the technician. Regarding the bvals, indeed the only thing you need to know (in most cases) is the b-value(s) used for your DWI acquisition, and this is something the technician can see directly on the console screen. The most intense image(s) in your nii file will be the so-called b0 images, with values in the bvecs file to be set to 0, while for all the other images you will have to write down the b-value you get on the screen (again, for simple cases; in particular multi b-value acquisitions this might change).

Last but not least, in my opinion it's always better to go back to the raw images as they come out from the scanner, since in your center there might be different acquisition schemes, and you or the tecnhician might get confused. You would then end up with an acquisition scheme that you might desperately try to fit to the data until the hell freezes, without obtaining any meaningful result... So, if possible, try to go back to the original raw images.

All the best!

leonardo


--
http://about.me/leonardo.cerliani
http://www.nin.knaw.nl/research_groups/k...

Leonardo Cerliani, PhD
BCN Neuro-Imaging Center
University Medical Center Groningen
Antonius Deusinglaan 2 (room 131)
tel. +31.363.8805
9713 AW Groningen - The Netherlands
Social Brain Lab
Netherlands Institute for Neuroscience
Royal Netherlands Academy of Arts and Sciences
Meibergdreef 47, 1105 BA Amsterdam, NL
___
{o,o}
|)__)
--"-"--
http://openlibrary.org/people/leonardoce...