Hi Mareen,
when you say the corrections are not visible, doo you mean the surfaces are still in the wrong place? Does the wm.mgz show the corrections? If so, then the edits you made didn't fix the underlying problem, possibly a topological defect. If you want to upload the data we'll take a look.
cheers Bruce
On Mon, 30 Aug 2010, Mareen Kussatz wrote:
Hi to all,
there are still correction problems after recon-all!
After recon-all not all of the corrections are visible???????
I corrected e.g. 10 slices. I deleted some voxels in wm.mgz as aux volume, non-white matter classified as white matter. I saved the aux volume and i startet recon-all! After running without errors, i checked in tkmedit. There were 5 of 10 slices corrected, but not the others???? With means there are still 5 slices of the previous corrected including some non-white matter classified as white matter! When i open the cor files for these slice, the corrections are visible!!
please help to find the bug
Best Mareen
-------- Original-Nachricht --------
Datum: Fri, 13 Aug 2010 11:38:01 -0400 (EDT) Von: Bruce Fischl fischl@nmr.mgh.harvard.edu An: Mareen Kussatz mareenkussatz@gmx.de CC: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] autorecon2
Hi Maureen,
if you exit tkmedit and reload the wm.mgz before rerunning recon-all are your edits in it? It shouldn't matter whether you edit/save in the main or aux volume.
cheers Bruce
On Wed, 11 Aug 2010, Mareen Kussatz wrote:
Hi to all,
after correcting white matter problems, we saved the wm as aux volume
and we tried also to save it as main volume. And than, we started recon-all -autorecon2-wm -subjid (subject file name). The process ends without any error for both conditions but after checking the tkmedit, there weren´t any corrections visible and actually there were no change at all.???
We just want to know if it is a syntax problem or if there is something
wrong with the freesurfer itself.
thanks and best regards.
Mareen Kussatz
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