Difference between revisions of "Healthy Volunteer Protocol Upload Process"

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   process_hv_data -subject_folder $Subject_Folder  #Loops over all task processing steps and creates QA documents
 
   process_hv_data -subject_folder $Subject_Folder  #Loops over all task processing steps and creates QA documents
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  Remove history files and replace paths/dates/names in text files
  
 
==Process_hv_data.py==
 
==Process_hv_data.py==

Revision as of 10:28, 12 May 2020

HV Bids processing requires

 pyctf
 General Utilities to interface with CTF data using python.  Also provides bids processing utilities.
 https://megcore.nih.gov/index.php/Pyctf  -  A more recent update will be coming available soon
 hv_proc
 Python scripts to extract and mark HV specific stimuli and validate trigger/response timing and data QA.
 **Open Access in development
 NIH MEG Bids processing
 Routines to convert the CTF MEG data into BIDs format using mne_bids and bids_validator
 https://github.com/nih-fmrif/meg_bids/blob/master/1_mne_bids_extractor.ipynb
 mne_bids
 https://mne.tools/mne-bids/stable/index.html
 pip install -U mne
 pip install -U mne-bids
 Afni
 Required for extracting HPI coil locations.
 https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/index.html

Bids Validator

 https://github.com/bids-standard/bids-validator

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 with the trigger data to label triggers and responses.


Processing on Biowulf

 To process the scripts on biowulf:
 pyctf & hv_proc must be in your conda path  (if necessary add filepaths to a .pth file in the conda site-packages folder)
 module load ctf
 module load afni

Processing Steps

 Acquire data
 Copy raw data to Biowulf: $MEG_folder/NIMH_HV/MEG
 Copy data to bids_staging: $MEG_folder/NIMH_HV/bids_staging
 sinteractive --mem=8G --cpus-per-task=4   #Start small sized server
 conda activate hv_proc 
 module load afni
 module load ctf  #Required for addmarks
 process_hv_data -subject_folder $Subject_Folder   #Loops over all task processing steps and creates QA documents
 Remove history files and replace paths/dates/names in text files

Process_hv_data.py

 Loop over the following scripts:
 CONVERT MRI FIDUCIALS TO TAGs >> get code name
 pyctf.bids.extract_tags $subjid_anat+orig.BRIK  > tagfile
 Process Tasks and assert ouputs match expected:
 airpuff_processing.py
 oddball_processing.py
 hariri_processing.py
 sternberg_processing.py
 gonogo_processing.py
 Calculate the noise level
 Scrub path info and history text files from the datasets to remove date and identifiers







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

Processing Scripts:

 Files have been compiled into a folder hv_proc
 This contains script interfaces into the megblocks package