Hi Louis, I've got the idea about the wm edits, but I have a related question. From what I see, that's a coronal cut at the level of the amygdala & basal ganglia. Isn't that the "gray area"? How relevant is to make edits in that area?
Thanks! Mihaela On Thu, Sep 19, 2013 at 4:07 PM, Louis Nicholas Vinke < vi...@nmr.mgh.harvard.edu> wrote: > Hi Francesco, > If it is the portion of the wm surface I have circled in red, then I'd > suggest looking a couple slices anterior and posterior to the current slice > and erase any other falsely labeled wm voxels on the wm.mgz, even if the wm > surf (blue line) doesn't currently include them. > > FYI, I've cc'ed the freesurfer list so others can chime in. > > -Louis > > On Thu, 12 Sep 2013, Francesco Siciliano wrote: > > Hi Louis, >> >> Thanks for the reply! I've attached a screen cap. Unfortunately, my >> cursor gets removed from screen caps, but I had the area highlighted with >> my cursor and the intensity was a value of 1, indicating that I had edited >> the area prior to running recon-all again. The area in question is the >> jagged portion of the WM surface in the lower center of the screen above >> the right temporal lobe). >> >> -Francesco >> ______________________________**__________ >> From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] >> Sent: Tuesday, September 10, 2013 5:55 PM >> To: Francesco Siciliano >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Editing WM >> >> >> Hi Francesco, >> Could you maybe send a snapshot of the brainmask and wm volumes where you >> are seeing this? >> >> If you deleted any voxels on the wm mask then they should be a value of 1. >> >> You might want to look at the ?h.orig.nofix surfaces to see if that area >> in question looks better (or at least different). Ultimately the position >> of the wm surface is what is important, not the presence or absence of wm >> voxels (in the wm.mgz) which basically just initialize the wm surfaces. >> -Louis >> >> On Mon, 9 Sep 2013, Francesco Siciliano wrote: >> >> Hi, >>> I've noticed that occasionally when I manually edit recons, the white >>> matter >>> surface will be drawn to include a portion of the volume where no white >>> matter >>> pixels are present. Therefore, when I go to correct the incorrectly drawn >>> surface, there are no pixels to delete under the white matter mask. It is >>> almost as if I have deleted the pixels already yet I have not and the >>> white >>> matter surface is still drawn to include an area where there are no white >>> matter pixels. Why could this be happening? Does it matter as long as >>> there >>> are no pixels in the incorrect area? >>> >>> Thank you, >>> >>> Francesco >>> >>> Francesco Siciliano, B.A. Research Assistant >>> Department of Child and Adolescent Psychiatry >>> The New York State Psychiatric Institute >>> Columbia University >>> 1051 Riverside Drive, Unit 74 >>> New York, NY 10032 >>> (212) 543-6155 >>> >>> >>> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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