Hi Mayuresh the "squiggly" stuff isn't necessarily a problem. You need to look at it in a different view, but it can be a region in which the surface is nearly paralell to the viewing plane to that it crosses back and forth a ton of times in a small patch.
cheers Bruce On Fri, 1 Apr 2011, Daniel G Wakeman wrote: > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
