Biowulf standard processing

Quick tutorial to generate most of the needed inputs for data analysis

General Setup

Mounting local computer to biowulf

 https://hpc.nih.gov/docs/hpcdrive.html

Configuring your bash shell environment

If editing your bashrc -- open two terminals in biowulf. If you misconfigure your .bashrc, you will not be able to log into biowulf. Having two terminals open allows you to fix anything that errors out.

Edit .bashrc file in your home drive

 umask 002   #Gives automatic group permissions to every file you create -- very very helpful for working with your team
 
 #Add modules bin path to access the MEG modules
 PATH=/data/MEGmodules/bin:$PATH
 
 ## Set up some aliases, so you don't have to type these out
 alias sinteractive_small='sinteractive --mem=8G --cpus-per-task=4 --gres=lscratch:30'
 alias sinteractive_medium='sinteractive --mem=16G --cpus-per-task=12 --gres=lscratch:100'
 alias sinteractive_large='sinteractive --mem=24G --cpus-per-task=32 --gres=lscratch:150'

Edit .bash_profile in your home drive

 #Set your default group (normally your default is your userID - which isn't helpful for your group
 #Type `groups`  to see which groups you are part of
 newgrp  <<YOUR GROUP ID>>

To Access Additional MEG modules

 #Add the following line to your ${HOME}/.bashrc
 module use --append /data/MEGmodules/modulefiles

General Processing Pipeline

First write out the appropriate events in the markerfile

 TBD - fill in items here

Convert Data to BIDS

 module load mne
 make_meg_bids.py -h   #Then fill in the required items

Processing the MRI related components

 #Generate Bounary Element Model / Transform / Forward model for source localization.  Check the help, there is a volume vs surface flag
 #This will write out the swarmfile (which can be editted) -- and prints out the command to launch the swarm job
 megcore_prep_mri_bids.py -gen_swarmfile -bids_root <<BIDS_ROOT>>  -swarm_fname <<SWARM_FNAME>>  -subject <<SUBJECT>> -run <<RUN>> -session <<SESSION>> -task <<TASK>>

Parsing Logfiles

Presentation Files: https://github.com/gjcooper/prespy