Hi Falk
I don't think it's possible to fix just one defect, unless Florent included some option that I am not aware of.
I also wouldn't worry too much about the filled.mgz. Make sure that the aseg.mgz and the ?h.white and ?h.pial are accurate cheers Bruce On Fri, 22 Mar 2013, "Falk Lüsebrink" wrote:
Dear FreeSurfers, I am processing some T1-weighted images of the human brain with an isotropic resolution of .5 mm using version 5.1. After mri_fill my hemispheres are separated nicely and the cerebellum is completely removed. However, looking at the filled.mgz, posterior and superior of the corpus callosum some residual of white matter can be found in the longitudinal fissure. It does not remain if I look at the conformed data, altough these leftovers are found in the wm.mgz of both datasets. As this does not happen using conformed data I assume that the cutting plane is not "broad" enough in case of higher resolution data or something related. Is there some way to tweak this? Secondly, I currently skip the -fix stage of recon-all completely while processing this data, but I would like to correct at least some of its defects. I already I have seen in the help of mris_fix_topology that it is possible to fix just one defect and I extracted the defects and their number of vertices using the defect-seg script. Is it possible to save the resulting surface, so I am able to correct the defects I want to consecutively? Best, Falk