dorahermes / ccep Goto Github PK

In the master_prepocessCCEP at least the following two issues need to be resolved.

1. Changing the data of bad channels to NaNs of deleting those channels from data. Most of them are not included in the data, only the channels that are marked as bad by visual inspection in MicroMed in the data

2. The removal of channel specific artifacts (changing to NaNs). Sometimes multiple channels have the same artifact onset, but a different offset, so this needs to be considered in the code.

Some scripts present in the folder script of the ccep directory are not necessary anymore, since all the code needed for each atlas (Destrieux, DKT, Benson and Wang) had been merged into one script (master_lookup_allfouratlases.m).

Currently, it analyses all peaks in all significant CCEPs, including the channels that are stimulated. Both peak find methods need a loop that only runs through channels that are not stimulated

cc_events now also contains e.g. artifacts, and also e.g. electrical_stimulation_site_num_1 and num_2 do not exist anymore, therefore code does not run properly anymore

@GiulioCastegnaro
Because in your analysis F01-F02 stimulation is not considered the same as F02-F01, while in my analysis it does, I think it is nice to add this option as a variable argument in the function for preprocessing. You and Dora made some slight changes for this in another script, so maybe you can add it into this function (I did a pull request for this function).

I think there are multiple ways to create a variable parameter/argument for a function. Including parse (but I don't know how this works), or 'switch nargin with case 2 and 3', but I think it might be best to use something like, but @dorahermes might have a better suggestion:

function [database] = ccep_load_database(database, top_path, varargin)
if isempty(varargin{1} OR varargin{1} == 'biphasic'
STEPS FOR ANALYSIS WITH AVERAGING ALL
elseif varargin{1} == 'monophasic'
STEPS FOR ANALYSIS WITH MONOPHASIC AVERAGING

I left some space in the function to put this into.