Hi,
How do you use ApplyTopup on data with phase-encoding along different axes? I know that the phase encoding is AP for the first acquisition and RL for the second. Because of the unknown sign-definition by the scanner manufacturer, I've tried the four following acquisitions, and none of them worked:
0 1 0 1
-1 0 0 1
0 1 0 1
1 0 0 1
0 -1 0 1
1 0 0 1
0 -1 0 1
-1 0 0 1
The readout time is identical for all acquisitions, which is why it is set to 1. Topup runs in all cases without any errors and log file looks ok.
> topup --imain=26_34_b0.nii.gz --datain=acq.txt --config=b02b0.cnf --out=topup_26_34
Also, the produced fieldcoeff maps look in all cases plausible, although a bit more noisy than usual.
However, applytopup crashes with the following error: terminate called throwing an exceptionAbort trap: 6
> applytopup --imain=26_,34_ --inindex=1,2 --datain=acq.txt --topup=topup_26_34 --out=26_34_correctedÂ
Thank you for your time, and I hope you can help me solve the problem,
Astrid
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