Thanks Nick. I am familiar with those pages, but none of those defects are apparent in this subject (e.g., no misclassifications, lesions, or failure to have the ventricles filled). The surface just appears to jump from one section to another over blank space (or over gm in the brainmask.mgz volume). Maybe I'll have to scrap this one. Thanks again.
-Derin
Derin,
The tutorial pages showing which defects to look for and how to fix them start here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData
this includes white matter edits:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits
Nick
On Fri, 2007-04-13 at 15:31 -0500, Derin Cobia wrote:
Here is a pic of the inflated.nofix, how do I know what to edit? I've checked the wm.mgz and it looks fine (at least I can't see any errors). Maybe I'm missing something, I've attached a shot of it as well. Thanks.
-Derin
look at the ?h.inflated.nofix to see what is causing the defect, and correct the wm.mgz manually to remove it. Jenni: can you point Derin
at
the appropriate wiki page?
thanks, Bruce
On Fri, 13 Apr 2007, Derin Cobia wrote:
The ?h.orig.nofix looks ok, meaning it follows the white-gray
boundary
appropriately. What should I try next?
-Derin
this is probably a topology fixing problem. Look at the
?h.orig.nofix
and see how it is On Fri, 13 Apr 2007, Derin Cobia wrote:
Did you mean wm.mgz? It looks fine. The orig surface is not good either. Here's a pic.
-Derin
> Hi Derin, > > What does the orig surface look like? and the wm? Are those > correct? > > Jenni > > On Fri, 13 Apr 2007, Derin Cobia wrote: > >> I have two subjects where the white surface does not follow the >> gray-white >> gradient (see attached pic for example). Is there any way to fix >> this? >> I'm assuming it has to do with the limitations of my scan too
(it's
>> FLASH >> data). I'm running 3.0.4, thanks. >> >> -Derin >> >> >
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