Dear Lulu,

I was trying to do pre-processing with our high angular resolution diffusion data from Siemens 3T.The acquisition was divided into 3 consecutive scans of 5 minutes each, to improve the comfort of the subject. They consisted of three blocks of 19, 20 and 21 orientations each. Each of these three acquisitions have one b0 images.

I read the manual of fsl's tool 'eddy' and 'topup', and I think that our data could be correctd(eddy current and suscepbility problem) by these two tools (Am I right?).

I extracted three b0 images, and tring to merge them together, but it gave me an error:

'fslMerge fault:Inconsistent orientations for individual images when attempting to merge.

Merge will use voxel-based orientation which is probably incorrect -*PLEASE CHECK*!'

I am not sure that if this problem is related to my gradient orientation, and if this problem would influence my following processing.

I don't think this has to do with your gradient directions. It sounds either like a round off error in the voxel size fields, or the storm/qform is different. I suggest you use fslhd to check those things.

Another problem is about the acqparams.txt file. Since we have three b0 images, and our phase encoding direction is R>>L, EPI factor is 128, echo spacing is 0.85 ms, I wrote the acqparams.txt file like this

" 1 0 0 0.108
-1 0 0 0.108
1 0 0 0.108
-1 0 0 0.108
1 0 0 0.108
-1 0 0 0.108"

Is this the right way to write the acqparams file for our three b0 images?

There is documentation about how to write these here http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP/Faq and here http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/EDDY/Faq.

However, it is not clear from your description if you acquired b=0 scans with reversed phase encode blips. Your acqparams file implies you have six b=0 files acquired R->L, L->R, R->L, L->R,  R->L, L->R in that order. Is that correct?

Jesper

  

Thanks in advance!

Lulu