Hi Jesper,

Thank you for your reply. I am still a little (a lot) confused. I was already following the instructions in the link you sent.

Specifically, is there any convention for what is called "blip-up" or "blip-down"? I.e. if I have data that are phase encoded in y,

but in one acquisition the direction is set to A->P is this nominally blip-down? I.e. labelled -1 in acqparams.txt, or does it 
not matter (so long as I'm consistent)?

I'm really confused by the values in the .bvec files. All that happened between one series and the next was that the phase encoding 

direction was rotated by 180 degrees (Siemens Skyra, standard diffusion sequence, 64 directions). Looking at the bvec files most, but not all, 
entries have the opposite sign.

Looking at our B0 data, I would say that it looks similar to the example data sets on the webpage, the distortions are reversed when the 

phase encoding direction is reversed. Also the output from Topup and Applytopup looks like it has removed the distortions from the 
original data - so something must be right!? 

Even though the field offset is derived from B0 images, the hifi output from Applytopup seems to suggest that the non-B0 images

are being correctly undistorted.....?

I have attached a couple of example bvec files which will hopefully demonstrate our confusion!

Best wishes,

Priscila

Dear Priscila,

> Hello. I have been asked to analyse a set of diffusion data and to do so I have been following the topup steps on the fsl website. I have come to the stage of "applytopup" and I am unsure about ordering of the data and the corresponding acqparams.txt file. I have been told that the data were acquired in 2 series, the first with blip down (A->P) and the second blip up (P->A), phase encoding was in the y-direction. Is this the correct way to interpret this?
> 
> My acqparams.txt file looks like this:
> 0 -1 0 0.065
> 0 1 0 0.065
> 

You should use the same acqparams.txt file for applytopup as was used for topup. The data should be organised such that all volumes in a file pertains to the same row in acqparams.txt.

I think that this page
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/ExampleTopupFollowedByApplytopup
explains it reasonably well.


> I also wondered whether having .bvec files with opposite sign (+/-) indicates that the data has not been collected using identical protocols. I understand that the numbers stored in the 2 .bvec files associated with each series correspond to the x, y and z components for each diffusion direction, but when I look at the values they differ in sign between the 2 series.....
> 

It does indeed sound as if your diffusion vectors are different for the two acquisitions. If you don't want do run eddy, i.e. if you rely on some other tools for movement and eddy current correction, that is not a problem. The diffusion signal is expected to be identical for v and -v (where v is a diffusion vector) so there is no problem with pooling the data and using either of the bvec files.

However, if you want to run eddy that is NOT a good situation. What you want for eddy to work is data with the same/similar diffusion signal but different distortions. This can be achieved by sign-swapping either the phase-encode direction or the diffusion-gradient direction. BUT if you swap both you have effectively swapped the distortions twice leading to similar/identical distortions in the two images and then there is no differential signal to drive the correction.

Jesper


> e.g. file1.bvec
> 
> 0 0.99999934 0 0.3456666666
> ........
> 0 ........
> ........
> 0 ........
> 
> e.g. file2.bvec
> 
> 0 -0.9999956 0 -0.3456670000 <- same magnitude, different sign
> ........
> 0 ........
> ........
> 0 ........
> 
> According to the applytopup help page, once I have used it I will be left with a single set of images, but which bvec file should I use?
> 
> 
> I would really appreciate your input on this.
> 
> Thanks in advance,
> 
> Priscila
>