1) As long as the remaining skull/scalp is not distorting the surfaces then it should not cause any problems with your analysis. Based on the snapshot you sent it looks fine, although be sure to check the entire volume of that subject.
2)The cvs_avg35 template should be located here: $FREESURFER_HOME/subjects/cvs_avg35 Not sure about the name.
-Louis
On Fri, 25 Nov 2011, Antonella Kis wrote:
Dear Bruce:
1).I am planning to do a GLM group comparison of FA/DTI data, using dtrecon. I checked all the recon-all results and I found that there is a small amount of scalp left for one subject (it appears only on 3 slices). I wonder if this small amount will affect my subject registration and if I should remove it or if I can continue my data analysis with this small amount of scalp left only for this subject (it shows only on few slices). Please see the attached image.
2). Is there a way to download the cvs template? Why this is called cvs_avg35? Does this mean that the age avg is 35 or what exactly means 35?
Many thanks, Antonella