Dear Scott,
> Hi,
> We encounter the following error message when attempting to run applytop with our BOLD data:
> terminate called after throwing an instance of 'TOPUP::ApplyTopupException'
> what(): ApplyTopup:: msg=Mismatched input files run01_mcf.nii.gz and field180.nii.gz
>
> We run the following command for topup, and the distortion corrected images look decent:
> topup --imain=merged_fields.nii.gz --datain=acquisition_parameters_merged.txt --config=b02b0.cnf --out=merged_results --fout=my_field --iout=my_unwarped_images
>
> then we use the following command, attempting to apply the correction to the entire BOLD timeseries, and that is when we encounter the error message:
>
> applytopup -i field180.nii.gz,run01_mcf.nii.gz -a acquisition_parameters_merged.txt -x 1,2 -t my_field.nii.gz -o discor
The input to the -t parameter should be merged_results, i.e. the combined image(for field)-text(for movement parameters) output.
>
> Is it the case that we need to motion correct the BOLD timeseries first (which we've done), and also do a linear registration of the different images (which we haven't done), prior to running topup and applytopup?
You should run the motion correct first. I am not sure what you mean by “linear registration of …”?
Jesper
>
> Thanks,
> Scott
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