Localizers

Context

The localizers are short cognitive tasks aimed at localizing some well known activities. The localizers and the anlyzing tools ahve been developed by Jean-Philippe Lachaux's team who nicely shared the code with us.

Start

The first localizers where done the 20/06/2018 with patient pat_02614_1073

tests

The stimuli are sent via "presentation" software.

Preprocessing

Fore each loca of each pat (pat_ccccc_mmmm)

create a folder in Donnees/Brutes:

pat_ccccc_mmmm_LocaName

Copy correspondingMicromed files and rename .TRC file as

pat_ccccc_mmmm_locaName.TRC

Create TTL file

Depending on the acquisition settings, the analysis requiers different preprocessing steps to create the TTL file.

In any case, the script Localizer_getTriggers.m needs to be run, if possible step by step.

This script is calling the script Localizer_getPatInfos that needs to be updated with the patient that will be run.

% if Nlx TTLs evts, read event and define idx start and end of each loca in Localizer_getPatInfos

% [TTL_Timestamps, EventIDs, TTL_ID, Extras, EventStrings, Header] = Nlx2MatEV(fullfile(NlxPath, 'Events.nev'), [1 1 1 1 1], 1, 1, [] );

% NlxEvt = [TTL_Timestamps' TTL_ID']; %µsec

% NlxEvt = NlxEvt(TTL_ID>0, :); %µsec

% NlxEvt = [NlxEvt (NlxEvt(:,1)-NlxEvt(1,1))*1e-6];

The outputs of the script are sanity checks figure and a .csv table that has to be used to create the .pos file.

With the .csv file you can compare the log file and the TTLs recorded. It is usefull to delete fake TTLs

Nlx2MM

This configuration is to be avoided if the triggers are not sent to Nlx and MM through a bipolar channel

TTLs are sent to Neuralynx that send them to Micromed:

TTL numbers are all presents and with correct number
Timings of TTL on Neuralynx are good
Timings of TTL on Micromed have up to 200 ms delay

Solution: take timing from Neuralynx and find the time delay between Neuralynx and Micromed to transpose the correct TTL timings to Micromed.

Find delay between Neuralynx and Micromed with the bipolar channels.

Neuralynx and Micromed in parallel

Trigger only via TTL

Find delay between Neuralynx and Micromed with a iEEG channel.

Trigger via TTL and bipolar voltage input

Find delay between Neuralynx and Micromed with the bipolar channels. For Micromed, there should be a bipolar trigger channel for each box in order to check the delay between the 2 boxes.

Micromed direct

Convert .TRC to ELAN

Launch.exe : F:\IR-IHU-ICM\Bureautique\EpiDBS\Epimicro\ExperimentProtocol\Localizer\DataLyon\Localizer - 21-02-2018\Localizer.exe

Load .TRC file: Fichier → Charger un fichier individuel

Select File and click on 'Convert to ELAN File

Remove the .TRC file from the loca folder

Create .pos,

This is the ELAN TTL file, that has to be created from the .csv file

3 columns separated with tabs, and save it as

pat_ccccc_mmmm_locaname_raw.pos

column 1 : sample

column 2 : TTL value

column 3 : 0

Electrodes names .eeg.ent

If some electrode have a number in the name, change the name frome the .eeg.ent to remove the number. Example: change Am2g1 to Amg1

Analyses

Run analysis

Select patient folder Fichier → Ouvrir dossier patient

Load the patient folder pat_ccccc_mmmm

Check:

Loca to analyze
"Execute the same Analysis for each Frequency Band"
"Generate Time Frequency Envelloppe"
Generate Maps (trialmat)
Generate Envellope Plots

Click on "Process Analysis"

Select chanels to analyze in the popup window

Wait until it's finished

Issues

If electrode has a number in the name, name cut at the first number: ex Ha2g1 will be Ha2
2 "l" in Envelloppe"
2 "l" ans 1 "p" in Envellope"

epimicro