View source for Mne bids pipeline

==Skip Background==
[https://megcore.nih.gov/index.php?title=Mne_bids_pipeline#Use_on_biowulf '''Use on Biowulf''']
==Intro==
BIDS is a standard specification for neuroimaging/physiology data. This currently includes at least: MRI, fMRI, DTI, EEG, MEG, fNIRS (and possibly ECOG/sEEG).  BIDS typically describes how RAW data is organized - and processed data is located in the bids_dir/derivatives/{AnalysisPackage}/{SUBJECT}/...  The main advantage is that common code can be generated to process data organized in a standard format.  Therefore, you should be able to import the bids data into any number of neurophysiological packages (MNE, Brainstorm, SPM, Fieldtrip, ...).  Additionally, standardized processing packages known as BIDS apps can be used to process the data in the same way as long as the data is organized in BIDS.

  BIDS (formal specs) >> MNE_BIDS (python neurophysiological BIDS) >> MNE_BIDS_PIPELINE (structured processing in MNE python according to BIDS definition)

===BIDS website===
  https://bids-specification.readthedocs.io/en/stable/

===Bids data organization===
[[File:BIDS_data_organization.png|1000px|Bids data organization]]

==MNE Bids==
MNE bids is a python tool to make and access neurophysiological data.  This tool is a branch of the MNE tools for neurophysiological analysis.
===MNE Bids website===
  https://mne.tools/mne-bids/stable/index.html

==MNE bids pipeline background==
Mne bids pipeline website:
  https://mne.tools/mne-bids-pipeline/
Full example:
  https://mne.tools/mne-bids-pipeline/examples/ds000248.html

===Processing===
All processing is defined in the config.py file.  This has hundreds of options to define the processing. 
  Here are some of the typical options:  https://mne.tools/mne-bids-pipeline/settings/general.html

Here is the full list of options:
  https://github.com/mne-tools/mne-bids-pipeline/blob/main/config.py

===Example Config===
(copy into a config.py text file and use)

Modify for use with your data - at a minimum: bids_root, conditions
  study_name = 'TESTSTudy'
  bids_root = 'YOUR_BIDS_DIR' #<< Modify
  task = 'TASKNAME'   #If this is left empty, it will likely find another task and throw an error
  l_freq = 1.0
  h_freq = 100.
  epochs_tmin = -0.1
  epochs_tmax = 0.2
  baseline = (-0.1, 0.0)
  resample_sfreq = 300.0
  ch_types = ['meg']
  conditions = ['stim']  #<< list of conditions
  N_JOBS=4  #On biowulf - leave this empty - it will set N_JOBS equal to the cpu cores assigned in sinteractive
  on_error = 'continue'  # This is often helpful when doing multiple subjects.  If 1 subject fails processing stops
  
  #crop_runs = [0, 900] #Can be useful for long tasks that are ended early but full file is written.

==Use on biowulf==
!!If you run into any issues - please let Jeff Stout know so that the code can be updated!!
===Make MEG modules accessible===
 #Run the line below every login 
 #Or add the following line to your ${HOME}/.bashrc (you will need to re-login or type bash to initialize)
 module use --append /data/MEGmodules/modulefiles

===Start interactive session with scratch to render visualization offscreen===
  sinteractive --mem=6G --cpus-per-task=4 --gres=lscratch:50  #adjust mem and cpus accordingly - subjects will run in parrallel

===Option 1: Create BIDS data from commandline===
  module load mne_scripts
  
  #Afni coregistered mri data  
  make_meg_bids.py -meg_input_dir ${MEGFOLDER} -mri_brik ${AFNI_COREGED}+orig.BRIK
  
        ## OR ##
  
  #Brainsight coregistered mri data
  make_meg_bids.py -meg_input_dir ${MEGFOLDER} -mri_bsight ${MRI_BSIGHT}.nii -mri_bsight_elec ${EXPORTED_BRAINSIGHT}.txt

===Option 2: Use CSV file to create BIDS (rest data only)===
Instructions and more info: https://github.com/nih-megcore/enigma_anonymization_lite  <br>
Fill out the csv with all of the appropriate entries <br>
  module load enigma_meg
  enigma_anonymization_mne.py -topdir TOPDIR -csvfile CSVFILE -njobs NJOBS -linefreq LINEFREQ -bidsonly  #Use the bidsonly flag if not anonymizing

==MNE BIDS Pipeline==
===Freesurfer Processing===
If you have already processed your freesurfer data - just copy or link the freesurfer data(see below).  You can also set the freesurfer directory in mne-bids-pipeline config file.  Alternatively, you can have the pipieline calculate freesurfer as part of the processing.  This will take time - adjust sinteractive session (see below).
====Already Processed - Copy Data====
  mkdir -p ${bids_dir}/derivatives/freesurfer/subjects  #If this folder doesn't already exists
  #Copy your subject from the freesurfer directory to the bids DERIVATIVES freesurfer directory
  cp -R ${SUBJECTS_DIR}/${SUBJID}  ${bids_dir}/derivatives/freesurfer/subjects

====Process Using MNE-BIDS-Pipeline====
  #your sinteractive session must include --time=24:00:00  so that the freesurfer processing doesn't time out
  
  #add the following step to your mne_bids_pipeline processing
  --steps=freesurfer

===Process data using MNE Bids Pipeline===
First make a config file: [https://megcore.nih.gov/index.php?title=Mne_bids_pipeline#Example_Config example]
  module purge 
  module load mne_bids_pipeline
  mne-bids-pipeline-run.py --config=CONFIG.py
        #Optional Flags
        #--steps=preprocessing,sensor,source,report  or all (default) - Can be a list of steps or a single step
        #--subject=SUBJECTID(without the sub- prefix)

====Example Output Images (from anonymized data - the pipeline does not anonymize)====
[[File : MNE BIDS PIPELINE output.png | 1000px ]]

==TEST DATA for biowulf==
This section provides some test data to analyze using mne-bids-pipeline.  Feel free to adjust parameters in the config.py after you run through the analysis the first time.  All of the analysis parameters are defined in the config.py provided.  Additional config.py parameters can be found above in [https://megcore.nih.gov/index.php?title=Mne_bids_pipeline#Processing Processing].
====Start Interactive Session====
  sinteractive --mem=6G --cpus-per-task=4 --gres=lscratch:50
====Copy and untar the data into your folder====
  cp -R /vf/users/MEGmodules/modules/bids_example_data_airpuff.tar ./
  tar -xvf bids_example_data_airpuff.tar
  
  #Add the bids_root to your config file
  echo bids_root=\'$(pwd)/bids_example_data_airpuff\' >> $(pwd)/bids_example_data_airpuff/config.py

====Load module and process the data====
  module load mne_bids_pipeline
  mne-bids-pipeline-run.py --config=$(pwd)/bids_example_data_airpuff/config.py

  #Copy this path for the next step
  echo $(pwd)/bids_example_data_airpuff/derivatives/mne-bids-pipeline/sub-ON02747/ses-01/meg/sub-ON02747_ses-01_task-airpuff_report.html

  #In another terminal download your results from biowulf
  scp ${USERNAME}@helix.nih.gov:${PathFromAbove} ./

  ''Open sub-ON02747_ses-01_task-airpuff_report.html in an internet browser to view the report''

==Setup for running on a headless server (no monitor attached)==
  #(add this to the bashrc and run **start_xvfb** before running):
  alias start_xvfb='Xvfb :99 & export DISPLAY=:99'
  export MESA_GL_VERSION_OVERRIDE=3.3
  export MNE_3D_OPTION_ANTIALIAS=false