>It looks like your slices are probably about 30 degrees from axial, is
>that considered "almost axial"?
Point taken. They are about 300degrees, and almost axial only in that it makes more sense visually to view them as axials than as coronals.

>I'd look very carefully at the coordinates for each slice, or at
>least two successive slices. Different scanners seem to stack
>oblique slices in different ways.
I did this, using the file_tool utility rick described to view the z-offsets. This gives zoffsets c/w those reported during to3d, 4.36446mm, which correspond to the z-projection of the axis of the slices: arcsin(4.36446/5)=60.1
If there are other utilities you'd recommend we use, please do!

We have had plenty of origin difficulties, but have worked out a fix -- I think-- by coregistering the spgr to the T1/func slab in SPM, which generates a rotated and zero-padded SPGR image, then 3dcopy of all three image types. Alll this to try ot avoid resampling the functionals! The images are then in register in the LR plane (though I can imagine this might not always be the case) but need to be translated in SI and AP. I managed this by viewing the AC in sagittal plane in T1 and SPGR, estimating the Nudge, applying it with 3drefit.
(For this dataset, that was -dyorigin 42mm and -dzorigin -91! We had similar offsets using de-oblique from Ziad and 3drotate.) Viewing the slices in their native plane puts the corresponding anatomy about halfway through the 5mm T1 for each SPGR 1mm slice, and the eyeball of the cross-reference looks OK. I imagine we'll also need to 3dAnatNudge as well.

However, the coordinate systems are still maddening to me. If you have a helpful reference please provide it and I'll try to educate myself. If Analyze format default is LAS, how does that relate to the SPM LPI order? Or, it just doesn't? Is the 'origin' top left corner of the viewed image? I seem to remember a switch for another command line that 'centered' the image origin, which suggested that origin woudl in that case be defined as volume center, but can't locate that now to ask you about it specifically, so maybe it's a figment....

Your thoughts about any of this are most welcome!

Very best
Alison Adcock