Dear freesurfers,

I am trying to convert a label that I have hand drawn into tksurfer into a volume file using mri_label2volume and succeed in transforming into a volume file but the volume looks splotchy and the ends are not connected , i.e. instead of a smooth bit of cortex I get disjointed bits in the cortex.. I found a similar problem being discussed previously in the archives  (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg01999.html) but I can’t seem to find the solution to it myself.

The steps I’ve used are:

Draw label in tksurfer, and save it and then use the following command.

mri_label2vol --label  test.label --temp norm.mgz -- reg mni152.register.dat -- proj abs 0 1 0.1 --subject --hemi lh --o test.label.mgz

When I load the resultant volume file, the surface is not smooth and there are holes in the surface. I’ve tried changing the delta values to quite small as well as setting the thickness at 2 with - - proj abs option, but this hasn’t made things better..

Has anyone encountered this problem before and knows how to solve it ? Am I missing something in the syntax?

Thanks very much in advance,

Prapti