Hi Pradeep,
it's impossible to tell if it's an error from a single slice. Things that look like holes may actually just be sulci if you page through a couple of slices. You should also be looking at the intensity volume (e.g. norm.mgz) not just the wm.mgz. If the surface follows the gray/white boundary everywhere then you are all set. The problems occur if for example a lesion causes the topology correction to put the surface in the incorrect location in order to get the correct topology.
cheers, Bruce On Tue, 6 May 2008, Pradeep Reddy Ramana wrote:
Hello Everybody,
This is Pradeep Reddy, just started my PhD in Medical Image Analysis and hence a newbie to FreeSurfer.
I've passed the auto-recon2 stage in the reconstruction procedure. Now I am trying to verify WM segmentation produced by the recon-all/auto-recon2, before I move on to further processing. The excercise given in the freesurfer tutorial ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits ) gives me one example on how to detect if there were a lesion and outlines how to fix it. But now when I observe the outputs I have, I am quite confused as to how to detect inaccuracies in the segmentation of white matter.
To make it more specific, I show you a slice of wm.mgh I have ( wmConfusion1 attached). Please look at the small yellow circle on the right. If I just follow the exercise, this looks like a lesion, as the yellow line cuts into it. but when I move up to next few slices, this hole opens up ( close to the green line ) giving me indications that it may NOT be a hole ( keeping in mind the inherent 3D nature of the MR image ). Also I am not sure whether there is an error in the image ( wmConfusion5 ) attched is an error is WM segmentation.
So my questions:
- What are the things I have to look for, while trying to verify the
WM segmentation ( after autorecon2 )? 2. Any thumb-rules laid out for this already? My googling was in fact in vain. 3. Any other tutorials/resources/books stating clearly what to verify, in different stages of reconstruction?
I am sorry to write a long email. Please be kind to help me in this regard.
Regards, Pradeep Reddy PhD Student, Simon Fraser Unviersity, Canada.