Dear Bruce,

I've uploaded 2 subjects, both with the same problems, it'll be great if you can take a look.

https://dl.dropboxusercontent.com/u/6070302/GUSTO_01_04002.tar.gz

https://dl.dropboxusercontent.com/u/6070302/GUSTO_01_04011.tar.gz

Yes, I've gone through the tutorials. I've added back wm to breaks where I think are appropriate. When that didn't help much, I've also tried adding control points, but it still didn't turn out well.

Thank you very much.

Kind regards, Joann

Date: Tue, 9 Sep 2014 08:28:07 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Help with pial boundary To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1409090827060.23927@nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

Hi Joann

it looks like some white matter is not being identified in the ?h.white surface. You need to diagnose why this is happening. It's probably an inaccurately corrected topological defect. Have you gone through the tutorials? You will likely need to add some wm voxels back in. If you upload the subject we'll take look if you like.

cheers Bruce On Tue, 9 Sep 2014, Joann Poh wrote:

...

Dear All,

I'm having issues with the pial surface - temporal lobe is being under-estimated (see wm-pial.png) where the red cross is. (Frontal lobe also has similar issues.) In wm.mgz, the white matter looks fine, as well as in aseg.mgz (see aseg-wm-pial.png) but just not the pial boundary.

What can I do to rectify this?

On a side note, I've tried adding control points (to the frontal lobe to solve a similar problem) but the pial boundary still does not cover the gray matter and I'm missing bits.

Thank you.

Kind regards, Joann