Hello,

I'm a relative newbie to AFNI group analysis coming from SPM. I have a dataset of subject functional runs (1 Func/subj) that were originally converted to .nifti format from their raw P files, and that is where I've started, the raw files are no where to be found. When I originally started using 3dcopy to convert to .BRIK/.HEAD, AFNI was echo'ing the warning about obliquity in the EPI's and Anat's.

After testing 3dWarp's deobliquing in a few different places in the preprocessing stream, decided to run afni_proc.py on all the subjects, deoblique the first subject, then use 3dresample to match the rest of the functional runs to the initial functional run. Observing the GLT results for just individual subjects after the 3dresample, everything looks how I would expect it to look with the functional underlay, and anatomical overlay matching very nicely. There is also clear evidence that the functional run was oblique because the noise activations outside the skull at low threshold run diagonally upwards off pitch.

My only issue has been running 3dttest++ for 20 or so subjects, my statistical output dataset appears to be dramatically larger (say 20-30% larger brain) then my template or 3dmean'd anatomical overlay. I thought it was possible that its just noise, or various inconsistencies in the +tlrc warp between subjects/runs which is giving the appearance of a larger brain due to varying overlap, but they're seem to be significant activations outside of the template/overlay using a high threshold, so I'm rather stumped.

I've used 3dinfo checked to make sure all of the runs have the same dimensions, not oblique, same voxel count, and are all warped to my desired template.

I've attached my 3dttest++ script as well