Hello,
I was hoping to get some feedback, to help solve this problem.
Registration of 2 MRI images(e.g.patientBrain to atlas).

Objective:
The main objective is to achieve a very good registration in the basal ganglia region.
Ideally the AC and PC of both images should be superimposed after registration.
Possible mismatch or poor alignment in cortical areas or skull is acceptable,
as those areas are not part of my study.

Approach:
I tried linear registration, which does a ok job, but does not
achieve the req. accuracy I wish to have.
I tried manual registration, which yielded also only ok results.
I tried point to point registraion, with no results due to lack
of information on how to use this tool. I think there are commandline tools to be used but
I was unable to find documentation on this.

Questions:
Which registration tool is most suitable for this kind of registration?
Is there a tutorial available other than the Manual on the website?
Does BioImageSuite have masking functionality? Meaning can I remove or mask
voxels to exclude them from calculation during registration.
Additional Info:
I use a 64 bit windows7 machine.
Any suggestion help solve this problem will be greatly appreciated.
Frank