I recently created a set of .nii images (containing probability values from an MVPA searchlight analysis run in matlab) which were then thresholded and converted to .img using imcalc.
When I load the .nii or the .img along with my T1 in SPM using check reg, they both appear in the same orientation (i.e. the .nii/.img is displayed as obliques slices covering the posterior potion of the brain).
However, when I try to load the .nii / .img in a program such a Mango or MRICro for the purpose of overlaying my pattern analysis success rate onto my T1, the .nii/ .img orientations seem lost and they are displayed as axial slices at the top of the brain.
Can anyone give me any pointers as to why this may be, and is possible to convert these to .mat to simply overlay in SPM or overlay 2 .imgs in SPM if there isn't a more straight forward solution?
Many Thanks. JB