issues and potential updates

[luschn]

Mainfunction input instead of script?

settings_filepath = 'C:\Users\lschneider\GitHub\Settings\LFP_time_frequency_analysis\Pulv_oculomotor\paper\lfp_tfa_settings.m';

Settings structuring

I would like to move from
Settings/analysis_type/project/version
to
Settings/project/version/analysis_type

LFP settings

folder management – quite some redundancy in the folder definitions

lfp_tfa_cfg.results_folder
lfp_tfa_cfg.proc_lfp_folder
lfp_tfa_cfg.analyse_lfp_folder
lfp_tfa_cfg.version

session info - very redundant in my opinion, for the sole purpose of defining pre- and post-injection blocks (which is defined in the data itself!)

lfp_tfa_cfg.session_info(sess) = ...
struct('Monkey', sitenames{sess}(7:9), ...
'Date', sitenames{sess}(end-11:end-5), ...
'Input', [mainfolder sitenames{sess}], ...
'Preinj_blocks', 0, ...
'Postinj_blocks', []);

State definition – dangerous redundancy here

lfp_tfa_states

reference hemisphere - lfp_tfa_cfg.ref_hemisphere still in the titles

lfp_tfa_cfg.ref_hemisphere = 'L'; %% has been replaced by lfp_tfa_cfg.contra_ipsi_relative_to='target'; %% or 'perturbation_site'

combining monkeys - new input
lfp_tfa_cfg.monkeys={'Cur','Lin',''}; %% added '' to combine monkeys

lfp_tfa_cfg.info_filepath %%currently not used (and i am not sure if we actually want to)
lfp_tfa_cfg.use_datasets %% not sure if this is used (or needed, because the exclusion happens before already, so redundant)

Seeing how the code works I am not sure what „any“ will do here
lfp_tfa_cfg.compare.reach_hands = {'any'};
lfp_tfa_cfg.compare.reach_spaces = {'any'};

Not quite sure why these inputs are relevant (or would ever change)

lfp_tfa_cfg.trialinfo.start_state = lfp_tfa_states.FIX_ACQ;
lfp_tfa_cfg.trialinfo.ref_tstart = -0;
lfp_tfa_cfg.trialinfo.end_state = lfp_tfa_states.TRI_END;

Not sure why not to take a defined epoch for this

lfp_tfa_cfg.baseline_ref_state = lfp_tfa_states.FIX_HOL;

% period of interest relative to onset of baseline_ref_state for baseline power calculation,
% Examples:
% 1. lfp_tfa_cfg.baseline_ref_period = [-0.5 -0.1]; considers the time
% period -0.5 s to -0.1 s from the onset of baseline_ref_state (i.e., if
% lfp_tfa_cfg.baseline_ref_state = lfp_tfa_states.CUE_ON, time period from
% -0.5 s to -0.1s from the cue onset is considered as baseline period)
% 2. lfp_tfa_cfg.baseline_ref_period = 'trial'; to consider the complete trial period
% for baseline power calculation

if isempty(lfp_tfa_cfg.baseline_ref_state)
lfp_tfa_cfg.baseline_ref_period = 'trial';
else
lfp_tfa_cfg.baseline_ref_period = [0 0.5]; % SET LIMITS OF baseline_ref_period here
end

Here I have no idea if htis makes sense at all

% which perturbation blocks to be considered for baseline power calculation
% set to 0 for considering only pre-injection blocks
% in case trials from a single perturbation block is analysed, the same
% block will be used for baseline calculation
% Examples:
% 1. lfp_tfa_cfg.baseline_perturbation = 0; only perturbation block 0
% (pre-injection) is used for baseline power calculation
% 2. lfp_tfa_cfg.baseline_perturbation = [0, 2]; combines perturbation blocks
% 0 (pre-injection) and 2 (post-injection), but is not recommended
% 3. lfp_tfa_cfg.baseline_perturbation = [2, 3]; combines perturbation blocks
% 2 and 3
if length(lfp_tfa_cfg.compare.perturbations) == 1
lfp_tfa_cfg.baseline_perturbation = lfp_tfa_cfg.compare.perturbations;
else
lfp_tfa_cfg.baseline_perturbation = 0; % set the perturbation block(s) to be used for computing baseline
end

% whether to consider choice (1) or instructed trials (0) in baseline power
% calculation
% in case, only either choice/instructed is being analysed, the trials from
% the analysed choice is used for baseline
% Examples:
% 1. lfp_tfa_cfg.baseline_use_choice_trial = 0; % consider only instructed trials
% 2. lfp_tfa_cfg.baseline_use_choice_trial = 1; % consider only choice trials
% 3. lfp_tfa_cfg.baseline_use_choice_trial = [0, 1]; % consider both instructed and choice trials
if length(lfp_tfa_cfg.compare.choice_trials) == 1
lfp_tfa_cfg.baseline_use_choice_trial = lfp_tfa_cfg.compare.choice_trials;
else
% set choice(1) and/or instructed(0) to be used for computing baseline
lfp_tfa_cfg.baseline_use_choice_trial = 0;
end