Dear Ged,
Thanks for the reply.

I went through the solution you suggested me. I checked(using the check Reg button in SPM) all my nifti files and found that many were not registered to the template(in fact almost all the images).The template which i was looking at was the Avg152T1.nii in the Canonical directory of SPM.  Then using the Display button i manually altered the RIGHT(mm),FORWARD(mm),UP(mm),PITCH(rad),ROLL(rad),YAW(rad) values to register my nifti images to the T1 template.Once the image looks registered, i press the Reorient Images button to save the changes in the respective header file. Even after the manual registration process, i was not 100% accurate in registration, but I believe that my registration were 95% correct. There were some amount of mis registration which i was not manually  able to remove(as the template image is smoothed image and it is difficult to look at the exact anatomical locations). Also  the VBM tutorial states that there is some amount of freedom as far as manual registration is concerned using the Display button.

To start the VBM analysis in baby steps,i used only 4 datasets(Rather than 20 subjects) from each group(There are 2 groups) and segmented the GM,WM using the VBM,as taught in the VBM manual.To eliminate any complexities for now, i did not add any nuisance.

I estimated my 2 Sample T test model and set the contrast as 1 -1. To check the brain within the bounding box, i initially set the p value to 1 and unfortunately, i found that the result is same as the earlier results.i.e the brain is outside the glass brain box.

I have attached the pdf which illustrates the  data quality check of sample homogeneity using covariance and the final result.

Please provide some solution

Thanks
Tanmay