yes I'm sorry, I'm new here. thanks a lot. claudia

2013/3/18 Bruce Fischl fischl@nmr.mgh.harvard.edu

Hi Claudia

can you cc the list so others can answer? I would view the ?h.pial and ?h.white surfaces over the norm.mgz and see if you think they are accurate. If not, there are various interventions you can take to correct them, that are detailed on our wiki

cheers Bruce

On Mon, 18 Mar 2013, Claudia Dacquino wrote:

Thaks a lot Bruce,

...

so I have to edit WM first, and then, what about grey matter? Do I have to paint all the None Sgmtn label points, or just the ones incorporating a piece of dura (so the very external ones)? Thanks, Claudia

2013/3/18 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Claudia

  the first thing to do is run recon-all -all to complete a recon.

Then you look through your data (surfaces overlaid on volumes) and determine if it is accurate (or accurate enough). If not, then control points are one possible intervention, and yes you would put them in regions of non-partial-volumed WM in which the intensity is < 110. This can cause the pial surface to move out as well as the white surface, but there are other reasons things can go wrong also such as topological defects and such.

  cheers
  Bruce

  On Mon, 18 Mar 2013, Claudia Dacquino wrote:

        Hi everyone,
        I'm a very new fresurfer user and I have to understand the

very simple basis of its use yet. So I have some maybe stupid questions about that. I heve to work on cortical thickness, so I suppose I have to complete the segmentation and then correcting CPs and Pial surface. The first question is if I have to edit CPs first and then, after running recon-all -autorecon2-cp -autorecon-3, to edit the Pial surface? The second is in the CPs editing have I to add ctrl pts in white matter areas that are less then 110 in voxel intensity? The last one is how do I have to correct the grey matter? Have I to paint all the None Sgmtn label points, or just the ones incorporating a piece of dura? Thanks a lot, and sorry for the very basic questions.

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