I've run some structural data through the VBM8 (SPM8 toolbox) and then run into trouble with running 3dttest++ on the resulting files. I've used this procedure before (since I prefer to operate in AFNI land). Essentially when I load the overlay stats over a mean image (made with 3dMean), I end up with the stats image looking considerably larger than the underlay (see below). Running nifti_tool on the files shows that they really aren't that different. Any tips would be appreciated.
nifti_tool -diff_hdr -infile ave.nii.gz stats.nii.gz
name offset nvals values
------------------- ------ ----- ------
dim 40 8 3 121 145 121 1 1 1 1
dim 40 8 5 121 145 121 1 6 1 1
vox_offset 108 1 3168.0
vox_offset 108 1 10560.0