Merge pull request #93 from Hzaatiti/operational-protocol

add kit read con using fieldtrip
Hzaatiti · Nov 22, 2024 · 1e15865 · 1e15865
2 parents 2726149 + 491474e
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diff --git a/docs/source/3-experimentdesign/demonstration/2-meg-biopsychology-class-tour.rst b/docs/source/3-experimentdesign/demonstration/2-meg-biopsychology-class-tour.rst
@@ -1,7 +1,7 @@
 Biopsychology class MEG demonstration
 =====================================
 
-Place and time: MEG lab in A2-008 at the 29th of November 2024, from 9:15 am to 10:40 am
+Place and time: MEG lab in A2-008 at the `29th of November 2024`, from 9:15 am to 10:40 am
 
 Agenda 85min
 ------------
@@ -36,10 +36,10 @@ Agenda 85min
 
 .. dropdown:: Show and discuss analysis results `20min`
     - Recap SQUID sensor operation, forward and inverse models, source reconstruction algorithms
-    - Experiment 1 analysis: `Resting state: Access link to Analysis Notebook <../../5-pipeline/notebooks/mne/resting_state_pipeline.ipynb>`_
+    - Experiment 1 analysis: `Resting state: Access link to Analysis Notebook <../../5-pipeline/notebooks/mne/fieldtrip_kit_restingstate.ipynb>`_
         - Show higher alpha power in eyes closed than in eyes open in the alpha band (8-12Hz)
         - Show that this difference is better seen in the occipital region
-    - Experiment 2 analysis: `Auditory vs Visual vs Motor experiment <../../5-pipeline/notebooks/fieldtrip/fieldtrip_audio_visual_motor.ipynb>`_
+    - Experiment 2 analysis: `Auditory vs Visual vs Motor experiment <../../5-pipeline/notebooks/fieldtrip/fieldtrip_kit_audio_visual_motor.ipynb>`_
         - Show auditory trials activating the auditory cortex
         - Show visual trials activating the visual cortex
         - Show motor trials activating the motor cortex

diff --git a/docs/source/3-experimentdesign/experiments/9-auditory-vs-visual.rst b/docs/source/3-experimentdesign/experiments/9-auditory-vs-visual.rst
@@ -2,19 +2,22 @@ Experiment example 9: Auditory vs Visual vs Motor stimulus
 ----------------------------------------------------------
 
 In this experiment, a random sequence of three stimulus is performed:
+
 - an auditory stimulus with a 200 Hz audio
 - a visual stimulus with a white flash appearing on screen
 - a motor stimulus requiring a button press
 
-Data is stored safely in NYU Box under `audio-visual-motor` file.
+Acquired datasets are stored safely in NYU Box under `audio-visual-motor` file.
 
 `MEG Data Directory <https://nyu.box.com/v/meg-datafiles>`_
 
 Author: Hadi Zaatiti <[email protected]>
 
 
+Download code from: https://github.com/Hzaatiti/meg-pipeline/tree/main/experiments/psychtoolbox/auditory-vs-visual
 
 .. dropdown:: Audio vs Visual vs Motor experiment
 
     .. literalinclude:: ../../../../experiments/psychtoolbox/auditory-vs-visual/auditory_vs_visual.m
-      :language: matlab
+      :language: matlab
+
diff --git a/docs/source/5-pipeline/5-notebooks.rst b/docs/source/5-pipeline/5-notebooks.rst
@@ -25,7 +25,7 @@ FieldTrip MATLAB Pipeline Notebooks
    notebooks/fieldtrip/fieldtrip_oddball_OPM_pipeline.ipynb
    notebooks/fieldtrip/fieldtrip_visual_crowd_preview_KIT_pipeline.ipynb
    notebooks/fieldtrip/fieldtrip_kit_attention_task.ipynb
-   notebooks/fieldtrip/fieldtrip_audio_visual_motor.ipynb
+   notebooks/fieldtrip/fieldtrip_kit_audio_visual_motor.ipynb
 
 
 

diff --git a/...ldtrip/fieldtrip_audio_visual_motor.ipynb → ...ip/fieldtrip_kit_audio_visual_motor.ipynb b/...ldtrip/fieldtrip_audio_visual_motor.ipynb → ...ip/fieldtrip_kit_audio_visual_motor.ipynb
diff --git a/experiments/psychtoolbox/auditory-vs-visual/README.md b/experiments/psychtoolbox/auditory-vs-visual/README.md
@@ -1,12 +1,3 @@
-# oddball
-MATLAB code for auditory oddball task with eyetracking.
-This is just a super simple example for how to play sound and record eyetracking using Psychtoolbox (http://psychtoolbox.org/) in MATLAB.
+# Auditory Vs Visual Vs Motor activity
 
-SPECIAL NOTE: The sounds in the folder 'SoundFiles' have not been RMS equalised!!!
-SPECIAL NOTE 2: There might be **many bugs!** 
-
-## Stimuli
-In one block, deviant sounds were presented against standard sounds. The standard sound is a 500-Hz pure tone, and there are two deviant types: white noise and harmonic tones (f0=200 Hz; 30 harmonics). All sounds are 500 ms long and with 30-ms cosine onset and offset ramps. (THEY SHOULD ALSO BE RMS EQUALISED.) In total, each deviant type was presented 10 times, for 20 deviant trials in total, and the standard type presented 60 times, resulting in an overall deviant probability of 25%. The inter-sound-onset interval is randomised between 3-3.5 second.
-## Procedure
-After calibration, subjects should be instructed to fixate their pupils on a fixation cross and listen to the sounds through headphones.
-Before the presentation of the first sound, there is a 15-second long resting state recording.
+This experiment provides three conditions visual, auditory and motor with a random permutation between them.