Dear Pedro
>
> I?m toward the correction of all EPI deformations due to movement,
> static field inhomogeneties and interactions of both:
>
> That?s why I have some questions regarding the toolbox ?Realign and
> Unwarp? and the tool ?Fieldmap? developed by Chloe Hutton and Jesper
> Andersson
>
>
>
> Realigning:
>
> 1. In the defaults of Realign one can set a mask which is
> automatically calculated as the inverse of the variance in each voxel.
> This is can be set when speech is performed or severe artifacts are
> present. Are usual EPI artifacts considered as severe?
>
I would say that this option would be used/useful mainly when "the artifact" introduces localised variance in the time-series. Speech is a good example of that since that would introduce varying distortions (mainly in orbito-frontal areas). I don't think in general that "normal" EPI susceptibility distortions would fall into this category. They do cause distortion-by-susceptibility distortions, which could in principle mislead realignment. However, for modern scanners I think this effect is too small to be a real problem (i.e. I don't think they will hugely bias movement parameters, but they will of course still cause residual movement related variance).
>
>
> Creating fieldmaps to unwarp EPI images
>
> 2. How can I input the VDM generated by ?FieldMap? file in the
> ?Realign & Unwarp? defaults
I am not sure I understand this question. If you are using the latest version of Unwarp (i.e. that which resides on the extensions page) you should be prompted for the *.vdm file.
> 3. Following the introduction of a VDM fieldmap in ?Realign &
> Unwarp?, does it make the same unwarping process that ?FieldMap?? I
> mean, does it use the same theory and procedures? Does apply a
> JacobianModulation too?
They are estimated in diferent ways (the static field is measured, and the rate-of-change of the field w.r.t. movent is estimated). Once they have been estimated they are used in the same way to resample the data. If you have used Jacobian modulation in the Unwarp-estimation (by setting that option in the defaults) Jacobian modulation will be used when resampling the images. The Jacobian will then be based on both the estimated rate-of-change fields and the measured "static" field. Note though that the latter is siply a voxel-wise scalefactor and will not influence the temporal variability.
Good luck Jesper
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