Dear Jesper,

 

I finished doing the processing of TOPUP and eddy with fsl. And also reoriented the bvec file after your reply.

 

I checked our diffusion direction by the code in fsl manual, and found that it's a a single shell high angular resolution diffusion imaging scheme (full sphere).

 

I usually processed the diffusion data with dsi studio, so this time I also loaded the eddy_corrected_data and re-oriented diffusion gradient table into dsi studio as before. But this time I found that no matter what reconstrucion scheme I use (GQI, QBI, or even DTI), generated fibers are all nearly straight lines (in the attachment). But when I imported the raw diffusion data, the resulting fibers were right.

 

So now I am checking if there was some thing wrong with my processing. Most parameters I used  were set as default except the acqparam.txt and the number of volumes.

 

Our acquistion was used with three same phase encoding directions (three b0 images, R>>L, withour blipping direction I think), so I wrote the acqparam.txt as below.

 

1 0 0 0.108
1 0 0 0.108
1 0 0 0.108

 

The contents in the index.txt file are 63 ones. I wondered that  if this was the correct way to write these files, and if it is enough to represent all information?

 

Many thanks for all your reply.

 

Best wishes,

Lulu