Topup acqparams.txt

[Ariadna Albajara Sáenz]

Dear all, When preparing the acqparams file to run topup, my txt file looks like this: 1 0 0 0.035 -1 0 0 0.035 The phase encoding direction in my first image from the file RL_LR_b0 is RL. Souldn't I put then in the first column a -1 instead of a 1? Since "when the frequency encoding gradient is negative, k-space is traversed from Right to left". The phase encoding direction in my DTI scans is RL and the DTI PS scan is the one with the reversed phase encoding (LR). The -1 should correspond to the reversed phased encoding image then (in my case LR) or the DTI scan with the phase encoding direction RL (since "when the frequency encoding gradient is negative, k-space is traversed from Right to left")? Is it better to put first the reverse phase-encoding image or the forward phase-encoding image? Thanks in advance,

[Do Tromp]

Hi Ariadna,

I would advice to send tool specific questions to the mail lists specific to those tools, in the case of topup, I'd suggest sending it to the FSL list serve.

All the best,

~Do

-- 

Do Tromp, MSc
Graduate student
Neuroscience Training Program
Kalin lab, Department of Psychiatry
University of Wisconsin - Madison, USA

www.dotromp.com