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 <fis...@nmr.mgh.harvard.edu> To: Rongxiang Tang <rongxiangt...@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 <fis...@nmr.mgh.harvard.edu> > To: Rongxiang Tang <rongxiangt...@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 <fis...@nmr.mgh.harvard.edu> > > To: Rongxiang Tang <rongxiangt...@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. > > > > > > > > > > >
_______________________________________________ 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.
