Hi Bruce,

Thank you very much for your response. I have two problems in particular that I am trying to solve. In one subject, a sulcus did not initially get identified, and after the fixes, it was only partially identified. I uploaded example images to http://nmr.mgh.harvard.edu/~nbilenko/seg/subj1_sag140.tif and http://nmr.mgh.harvard.edu/~nbilenko/seg/subj1_sag140_fixed.tif What could be causing that?

In another subject, some white matter in the temporal lobe did not get identified, even after adding points to wm.mgz. Example images are in: http://nmr.mgh.harvard.edu/~nbilenko/seg/subj2_hor140.tif and http://nmr.mgh.harvard.edu/~nbilenko/seg/subj2_hor140_T1.tif I suspect that this might be due to signal dropout due to sinuses - is that likely to be the case? Is there any way to fix it?

Thank you very much, Natalia

On Tue, Jun 15, 2010 at 5:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

Hi Natalia,

you need to figure out what's causing the error in order to understand whether a given fix is going to help. Sorry, I know that's a bit vague, but it really is a case-by-case thing, although there are only a smallish class of different types of problems (maybe 5 or so)

Bruce

On Tue, 15 Jun 2010, Natalia Bilenko wrote:

Hi all,

...

I have a question about fixing surface segmentation errors while doing an anatomical reconstruction. When I try to fix some white matter surface errors by deleting/adding points to wm.mgz and running recon-all -autorecon-wm, they sometimes get fixed only partially or not at all. I was just wondering if there is any way to predict whether a certain volume fix is going to alter a segmentation, or if the only way to find out is to fix the volume and wait for the results of autorecon2.

Thanks! Natalia

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