Hi Bruce

As far as I can tell this is not causing any problems downstream. Happy to accept the result as long as it is reproducible across different cases (which it appears to be)

Regards Nawaf

On 17 Oct 2013, at 11:29 pm, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Nawaf

is it causing you any problems? That is the current correct outcome, although we are considering whether to change the surface behavior in the medial temporal lobe. You shouldn't have to edit the wm.mgz as we detect those regions as non-cortical, and exclude them from the downstream analyses.

cheers Bruce

...

On Thu, 17 Oct 2013, Nawaf Yassi wrote:

Hi I would like to ask a question about the segmentation of the inferior horn of the lateral ventricle using freesurfer. I have noticed that the inferior horn is usually not filled in the wm.mgz file and excluded from the surface reconstruction (as demonstrated in the attachment). However, it is correctly labelled in the aseg file. Will I need to correct the wm.mgz manually and rerun recon-all or is this expected? Regards Nawaf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

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