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. -- There's more to life. Finding it is my job. -- [EMAIL PROTECTED] NOTICE my new contact Number in Canada: +1 604 720 2233
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