> 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'
> what(): x����
> 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).
am I right in thinking that these two volumes are acquired with the same phase-encoding? If so, you cannot use them to run topup.
The idea of topup is that you have two images where a given off-resonance field (the field that topup calculates) result in different distortions in the two images. Typically that is achieved by reversing the PE-blips in one of the images compared to in the other. The difference between the two images is the “error signal” that drives the estimation of the field.
> 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
I can’t say exactly what leads to the exception here, but if I am right in my assumption above “myout” will contain no valid information so it cannot work.
> Would you please tell me my error. Excuse me if my question seems silly but I'm new to FSL.
> Thanks so much