Hi Inês

it's tough to tell from a few images. I would guess it is a topological defect caused by a spotty segmentation. If you tar and gzip the entire subject dir and ftp it to us with the location of the problematic areas we will take a look

cheers Bruce On Mon, 14 Jan 2019, Borges Pereira Ines Isabel wrote:

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Dear FreeSurfer developers, I am reaching out again because the issue mentioned in the previous email. I have successfully edited many other subjects, but this one still eludes me. I am pretty sure the places where I placed the control points represent WM and I also clearly see excluded cortex. Since the pial surfaces do not update after WM editing, could you help me understand what the problem could be?

I am resending you the images, so you better understand what I mean.

Have a great day!

Best regards,

Inês Pereira

  On 16 Nov 2018, at 18:10, Borges Pereira Ines Isabel <inesb@student.ethz.ch> wrote:

Dear FreeSurfer developers, I am trying to obtain adequate pial surface boundaries. Unfortunately, on a few subjects, some grey matter is being excluded from the pial surface, at the temporal pole. I have attempted to solve this problem by adding control points and adding voxels on the wm.gz volume, so as to have FreeSurfer first update the wm boundary and then hopefully the pial surface. As you can see on the attached images, the control points were only partially taken into account and the pial surface was not updated. It would be great to get your support in understanding why this is happening.

I am using the following Freesurfer version on Centos: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Thanks! Best regards,

Inês Pereira

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