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
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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