Hi Mayuresh, I assume you are talking about the area in the posterior midline, where the pial surface seems to go 'squiggly'. You also seem to have a problem with the right hemisphere (left visually: I hate radiology ;)), where some dura seems incorrectly labeled as pial surface (although the grey matter is very difficult to see on this sequence/ at this setting).
To fix these I recommend this wiki page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits Good Luck! Dan On 2011 Apr 1, at 05:08 , <freesurfer-requ...@nmr.mgh.harvard.edu> <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. incorrect GM/WM surfaces (Mayuresh K) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Apr 2011 15:21:18 +1100 > From: Mayuresh K <mayureshk...@gmail.com> > Subject: [Freesurfer] incorrect GM/WM surfaces > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > <AANLkTi=bltokkzngth5sxhsqvmfruhakzg9u07xzw...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello freesurfer experts, > > I have successfully finished running the recon-all analysis without any > errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM > surfaces however look incorrect and I am not sure what may have gone wrong. > See attached screenshot from tkmedit. > Any suggestions how to fix this would be helpful. > > I have processed other datasets collected from the same scanner using the > same sequence which seem to have correctly identified the pial and > grey-white boundaries. I am using > freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1. > > Thanks, > Mayuresh > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110401/f494b1a2/attachment.html > > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: tkmedit ** brainmask.mgz ** (T1.mgz).png > Type: image/png > Size: 81386 bytes > Desc: not available > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110401/f494b1a2/attachment.png > > > ------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > End of Freesurfer Digest, Vol 86, Issue 1 > ***************************************** > > > 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
