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-request@nmr.mgh.harvard.edu freesurfer-request@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-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@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:
- incorrect GM/WM surfaces (Mayuresh K)
Message: 1 Date: Fri, 1 Apr 2011 15:21:18 +1100 From: Mayuresh K mayureshk.82@gmail.com Subject: [Freesurfer] incorrect GM/WM surfaces To: freesurfer@nmr.mgh.harvard.edu Message-ID: AANLkTi=BLTOKkZngtH5SxhsQvmFrUHakzG9u07Xzworn@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