Hi Clark, the phase encode direction is always lost since that
information is not represented in the nifti header. epidewarp.fsl always
assumes that the phase encode direction is in the row direction.
doug
On 11/13/2012 07:32 AM, Clark Fisher wrote:
> Hi everyone,
>
> I recently switched the phase encoding direction of the functional sequence I've been using from F>> H to R>> L and ran into a problem with epidewarp.fsl (in version 4). The unwarping was still happening along the F>> H axis in the new images where phase encoding was R>> L.
>
> (Note: I'm working with NHPs in sphinx position, but I'll describe my problem in standard coordinates to keep everything somewhat simpler)
>
> Because thought that epidewarp.fsl might be having a difficult time determining the phase encoding direction, I swapped the position of the F>> H and R>> L dimensions in my nifti file (going from LIP to IRP) and the dewarping now seems to work.
>
> Is there something going wrong in the unpacking such that the phase encoding information is lost? Also, is the phase encoding information stored anywhere in the nifti, so that I can automatically detect and correct cases like this?
>
> Thanks for the help,
> Clark
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Douglas N. Greve, Ph.D.
MGH-NMR Center
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