Difference between revisions of "Healthy Volunteer Protocol"

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====Healthy Volunteer Protocol - MEG component====
+
=Healthy Volunteer Protocol - MEG component=
 
This large scale study is being conducted to collect MEG on a large number of healthy controls with matched MRI/fMRI data
 
This large scale study is being conducted to collect MEG on a large number of healthy controls with matched MRI/fMRI data
 
The study is described in full detail in the manuscript: __Enter Link Here__
 
The study is described in full detail in the manuscript: __Enter Link Here__
   
 
=BIDS format / OpenNeuro=
====Datasets====
 
 
All data is be converted to BIDS format and uploaded to OpenNeuro as an open access dataset. https://openneuro.org/
*Somatosensory
 
*Sternberg working memory
 
*Hariri hammer
 
*Movie - "Growth" (Groei) https://www.imdb.com/title/tt6386160/
 
*Resting State - Eyes closed
 
*Auditory Oddball
 
*Go/No-go
 
 
====BIDS format / OpenNeuro====
 
All data is be converted to BIDS format and uploaded to OpenNeuro as an open access dataset.
 
 
Data triggers are cleaned using several routines listed below. These have been used to realign stimulus triggers to optical onset of the projector. Datasets that have logfiles have been merged
 
Data triggers are cleaned using several routines listed below. These have been used to realign stimulus triggers to optical onset of the projector. Datasets that have logfiles have been merged
 
with the trigger data to label triggers and responses.
 
with the trigger data to label triggers and responses.
   
  +
Information on data preprocessing prior to upload:
More details can be seen at:
 
 
https://megcore.nih.gov/index.php/Healthy_Volunteer_Protocol_Upload_Process
 
https://megcore.nih.gov/index.php/Healthy_Volunteer_Protocol_Upload_Process
   
  +
=Information on Tasks=
====Code====
 
 
===Datasets===
pyctf - core interface to CTF processing in python. Includes general bids related functions as well as general purpose MEG processing and MEG/MRI alignment.
 
  +
*Airpuff: Airpuff based somatosensory stimuli
hv_proc - Scripts for bids creation and QA of the datasets
 
  +
*Sternberg: Working memory task with 4 and 6 letter memory items presented visually
 
  +
*Hariri: Modified hariri hammer emotional processing task with positive and negative facial emotions and a subsequent emotional match
====Processing on Biowulf====
 
 
*Movie: "Growth" (Groei) https://www.imdb.com/title/tt6386160/
To process the scripts on biowulf:
 
 
*Resting: Eyes closed resting state
pyctf & hv_proc must be in your conda path (if necessary add filepaths to a .pth file in the conda site-packages folder)
 
  +
*Oddball: Auditory oddball identification task with standard tone, oddball target tone, and white noise distractor tone
module load ctf
 
  +
*Go/No-go: Visually presented go no-go with flanking distractors
module load afni
 
 
   
 
====Trigger Coding====
 
====Trigger Coding====
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sadmale,0x15
 
sadmale,0x15
 
sadfem,0x16
 
sadfem,0x16
 
Processing Scripts:
 
Files have been compiled into a folder hv_proc
 
This contains script interfaces into the megblocks package
 

Revision as of 11:08, 12 May 2020

Healthy Volunteer Protocol - MEG component

This large scale study is being conducted to collect MEG on a large number of healthy controls with matched MRI/fMRI data The study is described in full detail in the manuscript: __Enter Link Here__

BIDS format / OpenNeuro

All data is be converted to BIDS format and uploaded to OpenNeuro as an open access dataset. https://openneuro.org/ Data triggers are cleaned using several routines listed below. These have been used to realign stimulus triggers to optical onset of the projector. Datasets that have logfiles have been merged with the trigger data to label triggers and responses.

 Information on data preprocessing prior to upload:
 https://megcore.nih.gov/index.php/Healthy_Volunteer_Protocol_Upload_Process

Information on Tasks

Datasets

 *Airpuff:  Airpuff based somatosensory stimuli
 *Sternberg: Working memory task with 4 and 6 letter memory items presented visually 
 *Hariri: Modified hariri hammer emotional processing task with positive and negative facial emotions and a subsequent emotional match
 *Movie: "Growth" (Groei) https://www.imdb.com/title/tt6386160/
 *Resting: Eyes closed resting state
 *Oddball: Auditory oddball identification task with standard tone, oddball target tone, and white noise distractor tone
 *Go/No-go: Visually presented go no-go with flanking distractors

Trigger Coding

Oddball Task

Description: 3 sound stimuli presented to the participant. The participant attends to the "standard" tone stimuli (210 epochs) and is required to respond to the "target" tone stimuli (45 epochs) that are intermixed with the standard tone. Additionally a broadband noise stimuli is presented as a "distractor" stimuli (45 epochs).

 UADC003 - Left Ear auditory stimuli
 UADC004 - Right Ear auditory stimuli
 UADC005 - Participant response
 UPPT001 - Stimuli Coding (standard:1, target:2, distractor:3)

Hariri Hammer

Emotional processing task contrasting happy and sad faces. Shapes are used as neutral baselines. An initial "top stim" will be shown followed by a fixation crosshair. The subject is supposed to respond during the "choice stim" by pressing the left or right response button that corresponds to the face matching the "top stim" presentation.

 UADC006 - Left response
 UADC007 - Right response
 UADC016 - Projector onset
 UPPT001 - Parallel port stimuli

Temporal Coding (UPPT001)

 Top Stim
 Choice Stim
 Response Value

Stimulus Trigger codes (UPPT001)

 diamond,0x1
 moon,0x2
 oval,0x3
 plus,0x4
 rectangle,0x5
 trapezoid,0x6
 triangle,0x7
 hapmale,0xB
 hapfem,0xC
 sadmale,0x15
 sadfem,0x16