Problem with opening SPM-reoriented Nifti volumes

[jkmech]

Dear all,

Any help would be much appreciated. What I am trying to do is take a 3D Nifti brain volume, do a reorientation of it in SPM8 (an AC-PC alignment, also called a bicommissural alignment), then open the reoriented Nifti file in Image J in order to do tracings. But after I reorient the volume, every time I've tried to open it in Image J, it opens in the original, unaligned way (I have the Nifti Input/Output plugin installed). We've tried several things at this point (reslicing, creating an image using ImCalc in SPM) to no avail. The issue seems to be with ImageJ rather than SPM; we're guessing that SPM8 writes the new orientation into the Nifti header information, which ImageJ is not reading properly for some reason, but we could be wrong. Has anyone had this problem before or know how to possibly solve this? Again, any help would be much appreciated.

Thanks,

Jonn Kmech