when running mris_make_surfaces it's possible to manually set CSF,GM,WM and related thresholds.
now, what of the case where one simply doesn't have any CSF?
i.e. an ex-vivo scan.
I find it really hard to get a good pial surface despite much experimentation. It wants to contract the GM and make the outer edges CSF, no matter what I do.
I should say also that the T1 is really an MTR scan (nearly, but not exactly the same intensity profile) and the brains are macaque and marmoset.
I also find it hard to get the intensities such that frontal WM and e.g. the extreme capsule have WM range intensity. I'm happy to do manually, but I canot get the gradient from WM to GM right manually in these areas to satisfy mris_make_surfaces.
the data is really high resolution. it would be really great to capture the whole GM ribbon.
putting in noise at a sensible average intensity for CSF doesn't seem to help.
many thanks,
Colin