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 <vinke@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 [vinke@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




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