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:
1. 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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer