Dear Davide,

do you have any volumes with reversed phase-encoding that you can use to estimate the susceptibility field? If not, you can still run eddy, and I will assume that is the case here. I.e. I assume that all 260 volumes are acquired with the same PE-direction.

First, take a look at your b0 images. Do they look like they have been stretched/compressed in the A<->P direction? If so your acqparams.txt will have the line

0 1 0 0.05

If they look like they have been stretched/compressed in the left<->right direction, then it should instead have the line

1 0 0 0.05

Your index.txt file will simply be a text file with a single row of ones. You can cut and paste the below to generate the file 

indx=""

for ((i=1; i<=260; i+=1)) do indx="$indx 1"; done

echo $indx > index.txt

With reservations for any stupid “spell checks” that the mail program decides to do.

For the future you might want to consider interspersing a few more b0 volumes in among the dwis.

Jesper

On 1 Mar 2018, at 17:15, Davide Momi <[log in to unmask]> wrote:

Dear FSL experts,

I'm running eddy in my data acquired by Simens Avanto 1.5T where the first 4 volumes are the B0 files and the last 256 volumes are the Diffusion images.
I would like to figure out what should I enter both in the acqparameter.txt and index.txt files.

Thanks in advance

Davide