Thanks Matt. But I'm still a little bit puzzled about the "limits" of
field mapping correction. You wrote that it is good at "geometrical
distortion correction, but less good at correction of intensities from
signal stretching or compression". Aren't those just variations along a
continuum of the same underlying phenomenon?
thanks,
-MH
On Wed, 2010-10-13 at 11:44 -0500, Matt Glasser wrote:
> Hi Michael,
>
> It is certainly true that once signal from multiple voxels has been
> compressed into a single voxel, it is hard to put it back with a field map
> alone. For diffusion data, phase up / phase down corrections have a better
> chance of dealing with this issue, as you have the data both compressed and
> rarified and can figure out what the undistorted image would have looked
> like. It is not possible to do this with BOLD data, as you can't acquire a
> run and then a second run with the phase encode direction flipped and unwarp
> and average them (which is what happens with the diffusion data). That
> being said, perhaps if you acquired the slices of phase up and phase down
> interleaved with one of these faster TR sequences you could pull off phase
> up / phase down correction on BOLD data (though you would want to run slice
> timing correction first).
>
> If I recall correctly from a conversation Jesper and I had, R/L (or L/R)
> phase encode direction actually have the least severe distortions, but
> people don't like them because the distortions are not symmetrical. If you
> were most interested in stuff in the orbitofrontal region, it might make
> sense to use a phase encode that stretches rather than compresses this
> region (though of course other regions would be compressed instead).
>
> The field map is good at geometrical distortion correction, but less good at
> correction of intensities from signal stretching or compression (or outright
> loss).
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Michael Harms
> Sent: Wednesday, October 13, 2010 11:25 AM
> To: [log in to unmask]
> Subject: [FSL] effectiveness of field correction as a function of phase
> encoding direction
>
> Hello,
> Is the effectiveness of field correction for compensating for B0
> distortions at least partially dependent on the phase encoding direction
> used to acquire the BOLD or DTI data that is to be corrected?
>
> To use Siemen's parameter lingo, a "P>>A" phase encoding direction
> stretches signal from frontal cortex outward (anteriorly, into empty
> space), whereas "A>>P" (which is unfortunately Siemen's default)
> compresses signal from frontal cortex (i.e., moves frontal signal
> posteriorly, onto existing brain). It seems that once signal from
> multiple voxels is compressed into 1 voxel that not much correction
> would be possible... Is that indeed the case?
>
> thanks,
> -MH
>
>
|