Here are more detailed versions of my first two questions. 

1) I used tkmedit to look at the mean_func produced by a gfeat analysis of one subject's three functional runs overlayed onto the anatomical image produced by recon-all on that same subject(bert/mri/orig.mgz). The registration matrix I used was the anat2std.dat that was produced by running reg-feat2anat on all three of the feat analyses from the individual runs. When I did this I saw that the mean_func image was outside the boundaries of the anatomical image. Correspondingly, when I overlayed the zstat.nii.gz from the gfeat analysis onto the anatomical image I had activation outside of the anatomical image brain.

2)  Originally, I ran BBR on a subject that I had run Recon-all for.  I used BBR to register the example_func.nii.gz to the bert/mri/orig.mgz. I had BBR output an fsl.mat.  I then used ApplyXFM in fsl to apply BBR's fsl.mat to register the example_func.nii.gz onto a T1 image that had been created by converting bert/mri/brainmask.mgz into niftii with mri_convert. I tried it again, this time converting the orig.mgz to niftii. In both cases the example_func in T1 space image produced by ApplyXFM is rotated about 90 degrees and also inverted.  This is viewed in fslview,  The corresponding T1 images created by mri_convert are not.  What can I do to allow me to use BBR's fsl.mat within ApplyXFM?