Hi Andy,

control points only affect mri_normalize (and only if you run it with -f ../tmp/control.dat). You should rerun it. Make sure to save your brain volume so you don't have to fix the skull stripping. You can then redo the stripping via (from the mri dir):

mri_convert brain brain_mask.mgz mri_normalize -f ../tmp/control.dat -monkey orig T1 mri_mask T1 brain_mask.mgz brain mri_segment brain wm

cheers, Bruce

p.s. if mri_fill is still core dumping we'll give you a new version to try

On Wed, 22 Jun 2005, Andrew H Bell wrote:

Fellow FreeSurfers,

I have a few (more) questions regarding high-res monkey reconstructions. Forgive my naivete - I'm still quite new to this program:

I've managed to strip the skull and surrounding muscle tissue (mri_watershed -r 60 -h 15 -wat <in> <out> did the trick)

I am now trying to segment, fill and create surfaces.

Questions:

1. What is the relationship between mri_segment and control points? I've

added a whole whack of control points but they seem to have no effect on the segmentation. How do I influence the segmentation because I'm missing several areas of white matter.

2. For some reason, when I try to run mri_fill, I get a segmentation fault.

I'm using the following command:

mri_fill -PV 124 138 116 -CV 124 106 116 wm filled

I've also tried to enter the above values for the cutting planes in the EXPERT PREFERENCES (as per the manual) and use the interface to fill the white matter, create surfaces, etc. It runs to completion and splits the two hemispheres ok but lops off the top portion of the left hemisphere.

3. Getting back to control points, I've placed a bunch of control points in

white matter that seems to get missed. However, when I look at the result after adding these points, they are hanging in empty space (i.e., they don't seem to have any effect).

I'm sure this won't be the last of my questions. I appreciate all the help so far!!

Thanks!!!!

Andy

Andrew H. Bell, PhD Laboratory of Brain and Cognition National Institute of Mental Health 49 Convent Drive Building 49, RM 1B80 Bethesda, MD 20892 office: (301) 496-5625 ext.260 fax: (301) 402-0921 mobile: (202) 679-1279 bellah@mail.nih.gov