Hi Bruce,
The aseg is also problematic for several slices....I uploaded the subject dir on theMatinos center file drop...since the file is too big, I separated into two parts.
Thanks, Catherine
________________________________ From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Rongxiang Tang rongxiangtang@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 14, 2013 2:42 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem
probably not, although it's hard to say. If you upload the whole subject dir I'll take a look. How does the aseg look? On Thu, 14 Feb 2013, Rongxiang Tang wrote:
Hi Bruce,
I checked the skullstrip stage using this command:
tkmedit subjectid brainmask.mgz -aux T1.mgz -surfs.... and both of the brainmask and T1 images look fine.... the wm.mgz is problema tic, with some area missing..... I was wondering if I need to manually adding control points to solve the pro blem. Thanks, Catherine
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Rongxiang Tang rongxiangtang@yahoo.com Sent: Thursday, February 14, 2013 2:03 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem
Hi Catherine
that looks like something went wrong in the surface recon, not in the talairaching. Maybe a skullstrip problem? You need to investigate. Also, please cc the list so that others can answer!
thanks Bruce On Thu, 14 Feb 2013, Rongxiang Tang wrote:
Hi Bruce,
I attached two images...one is the target view and the other is the
moveable
view.
Thanks, Catherine
_
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Rongxiang Tang rongxiangtang@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, February 14, 2013 1:33 PM Subject: Re: [Freesurfer] talairach transformation troubleshooting problem
Hi Catherine
can you send us an image of what you are looking at?
thanks Bruce On Thu, 14 Feb 2013, Rongxiang Tang wrote:
Dear All,
When I was checking the talairach transformation output, I noticed that
some of the white matter was not included inside
the green line. Instead of drawing the green line to include all of the
white matter of the whole brain, it somehow only
includes the bottom half of the white matter of the brain.
Is there a way to fix that?
Thanks, Catherine
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.