when running mris_make_surfaces it&#39;s possible to manually set CSF,GM,WM and related thresholds.<div><br></div><div>now, what of the case where one simply doesn&#39;t have any CSF?</div><div><br></div><div>i.e. an ex-vivo scan.</div>
<div><br></div><div>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.</div><div><br></div><div>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.</div>
<div><br></div><div>I also find it hard to get the intensities such that frontal WM and e.g. the extreme capsule have WM range intensity. I&#39;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.</div>
<div><br></div><div>the data is really high resolution. it would be really great to capture the whole GM ribbon.</div><div><br></div><div>putting in noise at a sensible average intensity for CSF doesn&#39;t seem to help.</div>
<div><br></div><div>many thanks,</div><div><br></div><div>Colin</div><div><br></div>