[FieldTrip] Projecting connectivity data onto a template brain

Nakhnikian, Alexander Alexander_Nakhnikian at hms.harvard.edu
Fri Dec 2 19:17:35 CET 2016

Hello All,

I have some data that I need to project onto cortical slices/surfaces and I could use some advice. I've included a brief synopsis of my computation and the issue I'm having. Briefly, I'm generating data using a lot of code outside of field trip and the problem comes up with I try to import data returned by my home-grown code back into ft and use ft_sourceplot to visualize the data.

I'm looking at connectivity between contralateral cortical homologous regions as a validation of my implementation of an existing connectivity metric. Based on prior research, we know where the connectivity should be at a maximum. This is basically seed region analysis. The flow of computation is:

1) Create an eLORETA filter kernel using ft's built-in functions and a template brain (I don't have individual sMRI).

2) Find the MNI coordinates in ft's template grid that are both inside the brain and confined to the cortical mantle. Keep the corresponding entries in the imaging matrix and discard the rest.

3) Localize the EEG signals and reduce the 3D dipoles to a single trace using PCA with my own code.

4) Define a seed region and compute functional connectivity with every other voxel in the grid.

I've plotted the maximum connectivity versus the voxel location and the results look good but I need to project the data onto a cortical surface to visualize them and get publication graphics. I've tried taking a file returned by ft_sourceanalysis and replace the field .pow with the vector of connectivity values returned by my code and replacing the grid locations with the coordinates I get in my down sampled grid.

Here's the problem: When I try to interpolate the connectivity values to the template brain and plot the results I get activity spread equally throughout the entire brain. I suspect it's an interpolation issue since there are many more grid points in the template than in my data set. I've been trying to find a way to downsample the number of voxels in the template before interpolating but I haven't been able to.  Any input would be very much appreciated.

Thank you,


Alexander Nakhnikian, Ph.D.

Research Investigator

Boston VA Research Institute

Instructor in Psychiatry, Harvard Medical School
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