Hi Mozi,
1. Use the individual bvecs generated by dcm2nii. These will in general be different from the standard siemens, as they are rotated for slice angulation used in the acquisition.
2. It is true that, depending on the sequence, eddy current artifacts can be alleviated, but not fully removed. Eddy_correct will take care of any residual artifacts and also of subject motion that cannot be corrected during acquisition. Note that FSL5 now provides much better ways for distortion and eddy current correction (see topup and eddy toolboxes).
Cheers
Stam
On 28 Nov 2012, at 07:37, Liqin Yang wrote:
> hi experts,
> I'm new for DTI, and I have two questions for DTI data analyss.
> 1: For each subject, the bvec generated by dcm2nii or mriconvert are similar, but neither was same with the standard siemens directions provided by diffusion toolkit or others. Should i use individual bvec or standard siemens bvec? I tried both for fiber tracking, but the results are quite different.
> 2, I used both eddy_crrected (by FSL) and raw data for fiber tracking using traditional FACT, the results were different for quite a few fibers (the direction, length and streamlines couts). As my aim is to find the differences of fibers in two group, I wonder if the eddy_correct step will make my results more credible or suspect? A Siemens engineer told me that the system did some eddy current correction during the scan, but maybe the eddy_correct more precise?
> Thank you for any advice or discussion.
>
> Mozi
>
|