Hi Laura,

the surface can sometimes look like that when it is almost parallel to the viewing plane, so that it crosses that coronal slice back and forth many times. Take a look at it in a different view and see how it looks (like sagittal)

cheers Bruce

On Tue, 1 May 2012, Laura M. Tully wrote:

Hi Freesurfer Experts,

I am finding strange loops in the pial surface of my subjects and I'm not sure how to fix them. They do not seem to be caused by problems in the brainmask.mgz - the wm surface looks fine - and they do no seem to be caused by problems in the wm.mgz. What is the best way to deal with them?  I have attached a few tiff examples of these loops as visualized in the brainmask.mgz and accomanying saved points in the inflated surfaces so that you can see what I am referencing. Any advice you have would be most appreciated!

Best,

Laura.

-- Laura Tully Social Neuroscience & Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltully@fas.harvard.edu --My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/