I have some single-slice data that I want to overlay on an identically oriented anatomic image (identical image position (patient) DICOM attributes). If I just do to3d on the slice data and anatomic, the single slice data is not located in the correct spatial location

If I deoblique both volumes, the data is positioned correctly, but the single-slice is (as expected) now a series of strips

I can then 'reoblique' the single-slice data into the oblique-anatomic's orientation using the values in WARPDRIVE_MATVEC_INV_000000, but then I've resampled my data a couple times for what should amount to being largely just translations

Still, position looks about right at least.

However, if I use 3dAllineate and just apply the combined (WARPDRIVE_MATVEC_INV_000000)anatomic x (WARPDRIVE_MATVEC_FOR_000000)single-slice, I get a matrix of about

[ 1  0  0 | x]
[ 0  1  0 | y]
[ 0  0 -1 | z]

with no data ending up in my final image volume.


I have 6 single-slice 'volumes' that I've tried this on. 4 of them work fine (i.e. end up with data where I expect it and a translation-only transform matrix); 2 of them behave as described above. When doing to3d, all of the single-slice volumes issue:

*+ WARNING: Image Positions do not lie in same direction as cross product vector: ####

When #### is positive, everything seems to work ok. when #### is negative, they behave as described above.


Any suggestions on what I'm missing or what may be going on?

Many Thanks,
-C