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 <sa...@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.ur...@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 <sa...@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: >>> >>> https://github.com/nipy/nibabel/blob/master/nibabel/freesurfer/io.py >>> >>> cheers, >>> >>> satra >>> >>> On Mon, Jul 15, 2013 at 9:11 AM, Sebastian Urchs < >>> sebastian.ur...@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 >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it is >>>> addressed. If you believe this e-mail was sent to you in error and the >>>> e-mail >>>> contains patient information, please contact the Partners Compliance >>>> HelpLine at >>>> http://www.partners.org/complianceline . If the e-mail was sent to you >>>> in error >>>> but does not contain patient information, please contact the sender and >>>> properly >>>> dispose of the e-mail. >>>> >>>> >>> >> >
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