Hi Pegdro,

1) We did this to prevent noncortical regions such as the basal ganglia from corrupting the thickness measure through averaging. We the ?h.cortex.label we it is probably no longer needed.

2) The color maps are generic and useful for other things (e.g. curvature overlays, fMRI analysis or thickness differences) - the thickness values should be positive semidefinitie.

3) It's not the concoluted nature of the insula. It's the fact that extreme capsule is so thin that it frequently isn't very apparent on MR, and so there appears to be continuous gray matter from the basal ganglia into the cortex. I think version 4.0 fixes this.

Bruce

On Sun, 2 Sep 2007, Pedro Paulo Oliveira Jr wrote:

We are conducting a study and so far have analyzed 40 subjects using FreeSurfer.

We have some doubts regarding cortical thickness:

1.  Why the maximum value of cortical thickness in lh.thickness or
   

rh.thickness is 5.0 mm? We have case in which clearly the thickness is greater than that in some areas.

2.  In the thickness scale for one individual there are colors for
   

negative values. We don't see a topological or mathematical sense in negative thickness, is there any info on that?

3.  We found out that in many cases even in healthy subjects the Insular
   

cortex area presents 5.0 mm thickness in a great area. We think the algorithm may face difficulties in this area since its much convoluted. Is that assumption true?

Thanks in advance for the help.

Pedro Paulo Oliveira Jr

InRad - HCFMUSP