Hi,
If you are confident that the scans are already aligned well, then you do need to resample the fieldmap to match the EPI prior to applying fugue.
However, I would not normally recommend this strategy. In my experience the epi_reg tool gives better results. This does registrations between the fieldmap and structural image as well as the EPI and structural image (taking into account the fieldmap to undistort the image). It requires you to have a structural image that supports segmentation of WM, and also an EPI that contains some tissue contrast between GM and WM (this contrast doesn't have to be strong enough for a segmentation to work, but there must be something visible). If you cannot use the epi_reg tool then you can use fugue as you've suggested, but I would encourage you to try epi_reg if you have suitable images.
All the best,
Mark
On 21 Oct 2014, at 17:12, Ajay Kurani <[log in to unmask]> wrote:
> Hi Mark,
> I am about to use the FUGUE tool (all other preprocessing done and the map is aligned to the EPI using rigid transforms but not resampled to EPI space). My question is do I need to resample the fieldmap to match the EPI scan or can I just apply the field map directly using the following command:
>
> fugue -i epi --dwell=dwelltime --loadfmap=fieldmap -u result
>
> Thanks,
> Ajay
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