Hi Bruce,
 
well, there is an option called -correct_defect within mris_fix_topology, which is meant to correct just one defect at a time. However, after the defect is corrected one is getting a message like:
 
“TERMINATING AFTER CORRECTED DEFECT
 
no such file or directory”
 
I haven’t been able to figure out how to save this or if this is even possible. Maybe I am missing the correct flag to do so. May it otherwise be possible to remove certain defects from ?h.defect_labels or something similar?
 
The errors of the filled.mgz result in a faulty surface reconstruction of ?h.orig.nofix and every following surface like ?h.white and ?.pial in that area. Therefore I wanted to remove these in before and, if possible, automatically.
 
Best,
Falk
 
Von: Bruce Fischl
Gesendet: ‎22‎. ‎März‎ ‎2013 ‎19‎:‎14
An: ""Falk Lüsebrink"" <falk.luese@gmx.net>
Cc: FreeSurfer
Betreff: Re: [Freesurfer] Two questions regarding mri_fill and mris_fix_topology
 
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
>
>