Dear Scott,
> Hi Jesper,
> Thank you for the prompt reply! The inverted phase encoded volume is acquired at a different time (same scan session) than our BOLD run...but we have not registered those images--could that be the source of the problem?
>
> When I try the applytopup command as you suggested:
>
> applytopup --imain=field180.nii.gz,run01_mcf.nii.gz --datain=acquisition_parameters_merged.txt --inindex=1,2 --topup=merged_results --out=run01_mcf_dc.nii.gz
is field180 a fieldmap? If so I don’t understand the purpose of transforming it? If not, what is it? Is it really the run01_mcf.nii.gz that you want to correct. If so, leave out field180.nii.gz, set —inindex=2 and use —method=jac
Jesper
>
> I received the same error message:
>
> terminate called after throwing an instance of 'TOPUP::ApplyTopupException'
> what(): ApplyTopup:: msg=Mismatched input files run01_mcf.nii.gz and field180.nii.gz
> Abort trap
>
> applytop was run after this topup command:
> topup --imain=merged_fields.nii.gz --datain=acquisition_parameters_merged.txt --config=b02b0.cnf --out=merged_results --fout=my_field --iout=my_unwarped_images )
>
> Thanks again,
> Scott
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