Re: RE: [Freesurfer] automated parcellation: training set of Freesurfer

2007-10-02 Thread Bruce Fischl
by default we run both parcellations, so you should have them. Which to choose should be based on what your questions are. The Desikan-Killiany has in general larger units than the Destrieux one, but also anatomically different. As for your own training set, you'll need to create a set of manu

[Freesurfer] loading surface as a weighted graph

2007-10-02 Thread Michael Harms
Hello, This question is directed to the universe of FS users: Has anyone created a set of tools (e.g., Matlab) for converting FS surfaces into a (sparse) weighted graph structure? In principle, it doesn't seem like this will be too difficult to implement (making use of the some of the existing

[Freesurfer] Segmentation of MRI with cortical lesions

2007-10-02 Thread Martti Ilvesmäki
Hi, I'm using Freesurfer to generate the necessary surface-files for MNE software. However, when using the automatic segmentation on MRI from patients with cortical lesions, the segmentation does not work correctly. In one case the pial matter surface forms a deep hole (several cm) into the c

Re: [Freesurfer] Segmentation of MRI with cortical lesions

2007-10-02 Thread Bruce Fischl
Hi Martti, usually we manually fill the wm.mgz volume to correct for this type of lesion Bruce On Tue, 2 Oct 2007, Martti Ilvesmäki wrote: Hi, I'm using Freesurfer to generate the necessary surface-files for MNE software. However, when using the automatic segmentation on MRI from patients

Re: [Freesurfer] Segmentation of MRI with cortical lesions

2007-10-02 Thread Nick Schmansky
Martti, See this page for instructions on wm editing: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits Nick On Tue, 2007-10-02 at 15:00 -0400, Bruce Fischl wrote: > Hi Martti, > > usually we manually fill the wm.mgz volume to correct for this type of > lesion > > Bruce >