Dear Shania,
>
> Hello all,
> I am not sure whether this an error due to topup function or image.
> I am doing a longitudinal study analysis and I have applied topup for the wave 1 and wave 2 data. All were fine. But when applying topup on wave 3 I am getting a black image for fieldmap for the entire dataset. Scanner was upgraded for wave 3, hence there was a change in the acquisition parameter file(phase encoding direction and total readout time) and I have inputted accordingly. I am getting unwarped image for the entire data but I cannot figure out why I am getting a black image for the fieldmap. Maybe someone has some ideas why I am getting like this. I gladly appreciate every message!
> This is how I applied topup:
> topup --imain=sub-0015_merged.nii.gz --datain=acqparam.txt --confih=b02b0.cnf --fout=sub-0015_fieldmap.nii.gz --iout=sub-0015_unwarped.nii.gz
I am a little surprised to see that you haven’t specified the --out parameter. What are you intending to use the output for, and is it the --fout or the --iout output you are primarily interested in?
Are you sure that the --fout is actually black and that it is not only the settings in fslview/fsleyes that makes it look black?
Jesper
>
> Thank you in advance for all your help!
> Best regards,
> Shania
>
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