Hi,
I am trying to learn the VBM toolbox of SPM and I have strictly followed all the instructions from VBM8 manual(dbm.neuro.uni-jena.de/vbm8/VBM8-Manual.pdf) for Gray matter(GM) white Matter(WM) and Cerebro  spinal fluid(CSF) segmentation. I am trying to look at the difference in GM volume for 2 groups.

For the segentation, i have used all the defaults in Estimate and Write options in VBM8. After i have done the segmentation, i also used the "check data quality" to check my segmentation results. After smoothing, I used the 2 sample T test as my statistical model. I have strictly followed the manual for defining the parameters in this model. After running this model, i find that I have got a SPM.mat file in my analysis directory. After i Estimate my statistical model, I find that following images are generated in my analysis directory:
1. beta_0001.hdr
2. beta_0001.img
3. beta_0002.hdr
4. beta_0002.img
5. con_0001.hdr
6. con_0001.img
7. con_0002.hdr
8. con_0002.img
9. con_0003.hdr
10. con_0003.img
11. con_0004.hdr
12. con_0004.img
13. mask.img
14. mask.hdr
15. ResMS.hdr
16. ResMS.img
17. RPV.hdr
18 RPV.img
19. spmT_0001.hdr/img
20  SPMT_0002.hdr/img
21. SPMT_0003.hdr/img
22. SPM_0004.hdr/img

Also, when i define the contrast for group A vs group B (-1 1) and set the p value to  0.001(unc), then i find that the brain regions where i find significant difference in gray matter are not properly registered. Also, when i try to see only the brain for group A, I find that the brain is way out of the box and is not properly registered(I guess).
I have attached the images for your further understanding.
Following are my queries:

1.I am curious to know what these images mean which are generated after i have finished with the Estimation of my model.
2. Why am i facing this problem of getting improper results when i am strictly following the tutorial.Also, how to fix this problem.

Please reply and help

Thanks
Tanmay