[Freesurfer] inspecting images

Dear freesurfer users,

I am a beginner in freesurfer. I have run the recon-all command for all my images, but in some of them the program aborted before completing (and even if I try to re-run recon-all). After that, inspecting the segmentation with tkmedit and tksurfer, many images have small defects (like including pieces of dura within pial surface or excluding some white matter voxels from the white matter surface). I would like to ask:

1) What should I do to run recon-all approprietly? I have run with nifti images (.nii) - is that correct? 2) Should I correct all small defects observed in tkmedit and tksurfer for all images before running qdec?

Thanks a lot

Alfredo Damasceno