Re: [Freesurfer] Bad pial surface - continued

2010-05-10 Thread Bruce Fischl
Hi Ed, we can't help until we can accurately diagnose why it's happening. Have you checked for incorrectly fixed topological defects? cheers Bruce On Mon, 10 May 2010, Ed Gronenschild wrote: > Hi, > > I've mailed this once before and tried to solve a persistent problem. > Reviewing the result

Re: [Freesurfer] Bad pial surface - continued

2010-05-10 Thread Allison Stevens
Ed, do you want to send me the subject and I'll take a look? -- On Mon, 10 May 2010, Ed Gronenschild wrote: > Hi, > > I've mailed this once before and tried to solve a persistent problem. > Reviewing the results of recon-all I noticed that the derived pial > surface chopped away an unacceptable

[Freesurfer] Bad pial surface - continued

2010-05-10 Thread Ed Gronenschild
Hi, I've mailed this once before and tried to solve a persistent problem. Reviewing the results of recon-all I noticed that the derived pial surface chopped away an unacceptable amount of gm voxels. First of all I tried to manually edit some wm voxels, however with no success. Then I tried another

Re: [Freesurfer] Bad pial surface

2010-03-12 Thread Bruce Fischl
Hi Ed, we can't possibly diagnose this without seeing some images. cheers Bruce On Fri, 12 Mar 2010, Ed Gronenschild wrote: > Hi, > > Reviewing the results of recon-all I noticed that > the segmentation of wm and gm was OK but that > the computed pial surface chopped away an > unacceptable amou

Re: [Freesurfer] Bad pial surface

2010-03-12 Thread Allison Stevens
Ed, Usually a problem with the pial surface indicates a problem with the white surface and fixing the wm.mgz will fix the pial. But you said the wm segmentation is okay in the areas where the pial is a problem? What area of the brain are you finding this problem? Allison -- On Fri, 12 Mar 201

[Freesurfer] Bad pial surface

2010-03-12 Thread Ed Gronenschild
Hi, Reviewing the results of recon-all I noticed that the segmentation of wm and gm was OK but that the computed pial surface chopped away an unacceptable amount of gm voxels, too many to manually edit. Is there a way to cure this problem by choosing some options? I used version 4.5.0 on a Mac Int