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Computing Proximal Tissue Density index

Page history last edited by David Groppe 3 years, 2 months ago

It can be useful to identify which depth electrode contacts lie in white matter as these contacts can be used as a reference signal, ignored to increase your statistical power, or may merit separate study (Mercier et al., 2017). iELVis offers two ways to identify which electrodes lie in white matter. The simpler method is elec2parc.m which tells you the anatomical label of the voxel in aparc+aseg.mgz that each contact's centroid is in. You can get this by doing something like this:




A problem with this simple approach is that it does not account for uncertainty in the electrode localization procedure. In other words, we don't really know the anatomical location of contacts that lie on the border of two different types of regions. A way to deal with this is to compute the homogeneity of the anatomy around each contact's centroid and to only analyze data from electrodes whose anatomical location is highly homogenous. That is the approach taken by the "proximal tissue density" index (PTD) introduced by Mercier et al. (2017). PTD is an index reflecting the density of neocortical gray and white matter surrounding

a depth electrode that has its centroid either in the neocortical gray or in the white matter. It is:



Where nGray is the # of neocortical gray matter voxels and nWhite is the number of white matter voxels in the 3x3 voxel cube centered on the contact, as illustrated here:


If the contact centroid is not in white or neocortical gray matter, PTD = NaN.


Be careful when a contact is in the vicinity of subcortical structures as PTD is computed exclusively by taking into account surrounding neocortical gray and white matter voxels; no other tissue will be taken into account (e.g. Hippocampus, Amygdala...). Voxel labels are taken from the patient's aparc+aseg.mgz FreeSurfer file.


To compute the PTD index for all of a patient's electrodes, do something like this:

>>PTD_idx = getPtdIndex('PT001');


You can then plot the PTD index for all contacts like so:

>>figure(1); clf;
>>plot(1:length(PTD_idx.elec),PTD_idx.PTD,'-o'); hold on;
>>for a=1:length(PTD_idx.elec),
>>    fprintf('%d: %s %f\n',a,PTD_idx.elec{a},PTD_idx.PTD(a));
>>    h=plot(a,PTD_idx.PTD(a),'o');
>>    clickText(h,PTD_idx.elec{a});


Clicking on an electrode's marker will produce its name.




Mercier, M. R., Bickel, S., Megevand, P., Groppe, D. M., Schroeder, C. E., Mehta, A. D., & Lado, F. A. (2017). Evaluation of cortical local field potential diffusion in stereotactic electro-encephalography recordings: A glimpse on white matter signal. NeuroImage, 147, 219-232.

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