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
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.
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
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/**compliancelinehttp://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.
freesurfer@nmr.mgh.harvard.edu
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Louis Nicholas Vinke -
Mihaela Stefan