Re: [Freesurfer] Loading thickness data in python

2013-07-15 Thread Sebastian Urchs
t; faces_containing_vertex = np.nonzero((faces == > vertex_index).sum(axis=1))[0] > neighbors = np.setdiff(faces[faces_containg_vertex, :].flatten(), > vertex_index) > return neighbors > ``` > > cheers, > > satra > > On Mon, Jul 15, 2013 at 9:52 AM, Sebastia

[Freesurfer] Loading thickness data in python

2013-07-15 Thread Sebastian Urchs
Hi, I am trying to figure out how to load thickness data into python such that I would be able to identify the thickness at a given mesh node and also identify surrounding nodes. I searched the mailinglist and found this http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07307.html but

[Freesurfer] zones of zero thickness

2013-07-05 Thread Sebastian Urchs
Hi, I found that in some of my subjects there are - after manual correction - focal regions with zero cortical thickness. On closer inspection, I can see that the white matter and pial boundaries are touching in these regions - hence probably the zero thickness. My question is: should I manually