Greetings Fellow FreeSurfers,
I've been having some trouble skull stripping some hi-res monkey data and was wondering if anyone had some tips for a newbie:
The data is 256*256*256, 0.5mm3
I've normalized using the following:
mri_normalize -no1d -f ../tmp/control.dat -n 1 orig T1
and it yields a very nice set of brain images (good contrast between wm and gm). there is some very intense areas outside the brain (muscles) - i don't know whether that has an effect.
When I try "mri_watershed T1 brain", it runs (and takes a LONG time) to completion but the images are essentially untouched from the T1 images.
There are several warnings (e.g., mean intensity may be too low) which it looks like it tries to adjust for but again... no success.
Any help is greatly appreciated!!!
Andy
Andrew H. Bell, PhD Laboratory of Brain and Cognition National Institute of Mental Health Bethesda Maryland USA