I have also EPI which is just in one direction and I'm trying to correct it but at the end of applytopup I recieve an error like:
terminate called after throwing an instance of 'TOPUP::TopupFileIOException'
Abort (core dumped)
I think I have done something wrong in preparing the arguments. What I have done so far is as follow:
1.I have extracted first two b=0 volumes (output=b0.nii) and set the acquisition parameters as 0 1 0 1 in two rows (aqsprm.txt)
2.Then I ran topup on b0.nii as normal (output=myout).
3.Then I ran applytopup on my main EPI image (myepi.nii) with this syntax:
applytopup --imain=myepi.nii,myepi.nii --inindex=2,1 --datain=aqsprm.txt --topup=myout --out=corrected --method=jac --interp=spline
Would you please tell me my error. Excuse me if my question seems silly but I'm new to FSL.
Thanks so much