Hi Satra,

thank you very much - this has been tremendously helpful. I have now identfied neighbouring verteces within a certain distance using networkx and all_pairs_dijkstra_path_length.

I would now like to create my own curvature overlay (similar to the thickness file) by assigning non-zero values to neighboring verteces to a selected vertex and zero to others. My question is: is there any way I can save a numpy array to a "morphometric" file using nibabel or a different package?

Thank you very much,
Sebastian


On 15 July 2013 15:58, Satrajit Ghosh <satra@mit.edu> wrote:
hi sebastian,

you simply need to read the geometry file and the morphometry vector and the two pieces will give you what you need.

the geometry file gives you the relation between vertex indices via the faces array.

```
def return_neighbors(faces, vertex_index):
    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, Sebastian Urchs <sebastian.urchs@gmail.com> wrote:
Hi Satra,

thank you very much. I believe I have to rephrase my question as I didn't completely think it through. I need to find neighboring vertices to a specified vertex and then read out their thickness values. I don't think I can do this directly from the morphometry vector that pysurfer gives me.

Thanks again, I'll send another mail to the mailinglist.

Best,
Sebastian


On 15 July 2013 15:22, Satrajit Ghosh <satra@mit.edu> wrote:
hi sebastian,

please take a look at pysurfer (https://github.com/nipy/pysurfer) and nibabel (https://github.com/nipy/nibabel).

the relevant code is here:


cheers,

satra

On Mon, Jul 15, 2013 at 9:11 AM, Sebastian Urchs <sebastian.urchs@gmail.com> wrote:
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 this unfortunately did not solve my question as I was unable to find a downloadable version of pymgh.

Is there some python package that you could point me to and that allows me to load thickness data and do analysis in python?

Thanks in advance!
Sebastian

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