search

Kleen-Lab / OPSCEA

From the Kleen Lab at UCSF (http://kleen.ucsf.edu). Software for heatmaps of seizure activity projected onto reconstructed brains (Omni-Planar and Surface Casting of Epileptiform Activity). PAPER: https://doi.org/10.1111/epi.16841, VIDEO EXAMPLES: https://www.youtube.com/playlist?list=PLGmfrsRwdva-WKwqLyWwcZxE0f_MA9vIL
Other
8 stars 7 forks source link

Acccurate views seem to depend on non accepted meshes #8

Closed raphaelchristin closed 1 year ago

raphaelchristin commented 1 year ago

In OPSCEA, there are 7 accepted mesh terms for the surfaces: Rcortex, Lcortex, Rhipp, Lhipp, Ramyg, Lamyg, wholebrain. Some of our data contains other meshes, like Rins, Lins, Rcin, Lcin. These meshes raise a warning: ATTN: Row X defined as surface but does not contain an accepted mesh term, which seems to be ok (although it would be better to specify that the problem is related to extra unaccepted meshes instead of no accepted meshes), but there is an issue when trying to fix the warning.

Removing the unaccepted meshes from the params file causes the visualization to not be fitted on the brain of the patient. We could fix the warning to not show in the cases where the terms are necessary for the visualization but I would want to investigate why we need the terms if they are not accepted.

raphaelchristin commented 1 year ago

It seems that we could just add these terms as accepted terms

raphaelchristin commented 1 year ago

I will add the mesh terms as accepted as they are a part of our data. It does not seem logical to warn the user about mesh terms that are an essential part of our data