Hi-

That is a pretty extreme obliquity!

What is obliquity? There are coordinates defined in scanner: a grid where the z-axis runs along the bore, and then x- and y- planes are perpendicular to that. However, sometimes a person's head isn't aligned conveniently to that, and fitting a "shoe box" FOV would be more convenient if slices were made on a different grid-- that is, one defines a new grid whose x-y plane differs from that of the scanner. These new coordinates are called "oblique coordinates".

In oblique coordinates, the brain slices are probably roughly aligned with the x-y plane (where, in the scanner coordinates, the standard brain planes are probably at an angle to the x-y coordinates).

For visualization purposes, the oblique coordinates are convenient. However, for relating to other data sets (which might not have been acquired obliquely) or likely with the DWI gradients (which *I believe* would be acquired in terms of scanner coordinates), using the scanner coordinates makes most sense.

How do we convert between the oblique coordinates and scanner coordinates? We use matrix transforms (yay!). The "oblique" DWI dataset that you have has information in its own header to transform itself into the scanner coordinates. If you run

3dWarp -deoblique -prefix DSET_SCANNER_COOR DSET

then DSET_SCANNER_COOR will show your dataset on a new grid, whose x-, y- and z-values match with the scanner. It will probably appear to be at a fairly steep angle to standard view planes (based on what appears to be your dset's amount of oblique angulation). But there you have it.

Note that the price you pay for acquiring your data on oblique coordinates is that, when you return your data to the scanner coordinates, you re-grid your data, which is a process that inherently involves smoothing, because the dset values have to be interpolated.

Re. eddy current correction: how are you performing that? With AP-PA (blip up/down) correction, for example using DIFFPREP in TORTOISE (which woudl likely involve using the anatomical volume as a reference)? Or are you applying a field map, and if so, was this acquired on the same oblique coordinates?

The phase encode axis of a dset is defined along the acquired slices, so therefore in oblique coords.

--pt