Dear Mahmoud,
> I know that this has been discussed a lot (I searched the forum) and also has been explained in the FSL wiki but it would be great if someone could verify that what I am doing here is correct and help with my anxiety!
>
> I have diffusion data in the following format for each subject:
>
> 7 b0 volumes + 89 b700 volumes acquired together in AP direction
> 7 b0 volumes + 90 b2000 volumes acquired together in PA direction
why have you chosen to acquire all b700 volumes with one PE-direction and all b2000 with another? There is nothing necessarily wrong with that, but I would be a little concerned that you introduce a systematic difference between the two shells. I think for the future a better strategy would be to either chose a single PE-directions for all scans (except for a couple of b0 volumes for topup), or to acquire both shells with an equal mixture of AP and PA.
>
> I concatenate the b0 volumes from AP and PA acquisitions for topup and use an acqp.txt file as below ( it has 7+7=14 rows):
> 0 -1 0 0.06825
> 0 -1 0 0.06825
> 0 -1 0 0.06825
> 0 -1 0 0.06825
> 0 -1 0 0.06825
> 0 -1 0 0.06825
> 0 -1 0 0.06825
> 0 1 0 0.06825
> 0 1 0 0.06825
> 0 1 0 0.06825
> 0 1 0 0.06825
> 0 1 0 0.06825
> 0 1 0 0.06825
> 0 1 0 0.06825
What you are doing is correct and will give you correct results, but it is definitely overkill. The purpose of running topup is to get an estimate of the susceptibility off-resonance field, and you don’t really need all eight pairs for that. I usually recommend using a single pair (or at a stretch two pairs) so your input to topup would only contain two volumes and your acqp.txt would be
0 -1 0 0.06825
0 1 0 0.06825
But as I said, there is nothing wrong with you have done. It just takes unnecessarily long to run.
>
> For eddy, I use the same acqp.txt as topup and the output results from topup. When the input image to eddy is the volumes in AP direction I use an index file containing 96 (7+89) 1s and when the input image is the volume with PA direction the index file contains 97 (7+90) 1s.
I would recommend running eddy on all the data simultaneously rather than in two batches. In that case you would concatenate your AP and PA files into a single 4D file, and also do the same with the bvals and bvecs files (you can use the bash paste command). If you use your acqp.txt file above the index file should then be 96 1s followed by 97 8s. If you chose to use my acqp.txt file instead it should be 96 1s followed by 97 2s.
Good luck Jesper
>
> Please let me whether what I am doing is right or wrong.
> Thank you!
> Mahmoud
>
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