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