See the HCP Pipelines paper:
http://www.sciencedirect.com/science/article/pii/S1053811913005053
You need to make a unique warpfield volume for each frame that contains
the motion correction and the field map correction.
You can convert a field map to a warpfield with fugue by first saving a
shift map and then converting that to a warpfield with convertwarp. You
can then concatenate each motion correction matrix to this warpfield with
convertwarp, making a unique warpfield volume for each image.
Peace,
Matt.
On 10/7/13 11:54 AM, "Torsten Rohlfing" <[log in to unmask]> wrote:
>Hi All:
>
>In our rs-fMRI data, we would like to correct both B0 field-induced
>distortion (using FUGUE) and motion (using mcflirt?), but in a single (!)
>interpolation operation.
>
>Is it possible to perform a single reslice using the concatenation of
>fieldmap-based unwarping and rigid motion transformation? Would we do
>this using flirt, can fugue do it, or would we need to do some more
>involved transformation computations?
>
>Hope this makes sense. Thanks!
>
>Torsten
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