The acquisitions are SPGRs, taken on either a GE 3T or 1.5T (I'm not exactly sure, I'm new to the job). Yea, in a lot of areas the dura is adjacent to the grey matter. Those are certainly the problem areas - in most other areas the segmentation is excellent. I'm not sure of the resolution.
-----Original Message----- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Tue 11/6/2007 8:49 PM To: Watson, Christopher Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Manual edits to aseg.mgz/brainmask.mgz Hi Chris, what type of acquisition are you using? Dura can be really hard to deal with, as it can look just like gm, depending on your MR parameters, and it is can also be physically adjacent to gm. That said, it's only usually a problem in localized areas. What resolution is your data? We have some newer sequences and code that avoid the dura, but they are by no means standard (and we only have them for Siemens). cheers, Bruce On Tue, 6 Nov 2007, Chris Watson wrote: > Hello all, > I was wondering if there is a quick way to make edits to multiple slices of > the aseg.mgz (or the brainmask.mgz) volume. > > Specifically, I am working on my first subject, and it seems that on almost > every slice, pieces of the dura/skull/arachnoid/what-have-you get segmented > as cortex (less often, pieces of dura are included within the boundary of the > pial surface). I've worked on some slices by manually removing/de-segmenting > the pixels that need to go, but this is proving to be extraordinarily > time-consuming (some of the slices I've worked on can take 10 minutes easily; > perhaps I am obsessing too much, but am trying to get it as close to perfect > as it should look). For over 100 slices, even 5 minutes/slice of editing will > take several hours. I tried changing the mri_watershed parameter on another > subject, but that didn't seem to fix anything. > > Any tips to save me hours will be greatly appreciated. > > -Chris > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
