Biowulf standard processing: Difference between revisions
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== General Setup ==
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 ===
# Parsing Logfiles▼
#Add the following line to your ${HOME}/.bashrc
module use --append /data/MEGmodules/modulefiles
== General Processing Pipeline ==
=== First write out the appropriate events in the markerfile ===
TBD - fill in items here
=== Convert Data to BIDS ===
module load mne
make_meg_bids.py -h #Then fill in the required items
== Processing the MRI related components ==
#Generate Bounary Element Model / Transform / Forward model for source localization. Check the help, there is a volume vs surface flag
#This will write out the swarmfile (which can be editted) -- and prints out the command to launch the swarm job
megcore_prep_mri_bids.py -gen_swarmfile -bids_root <<BIDS_ROOT>> -swarm_fname <<SWARM_FNAME>> -subject <<SUBJECT>> -run <<RUN>> -session <<SESSION>> -task <<TASK>>
Presentation Files:
https://github.com/gjcooper/prespy
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Latest revision as of 17:40, 13 February 2024
Quick tutorial to generate most of the needed inputs for data analysis
General Setup
Mounting local computer to biowulf
https://hpc.nih.gov/docs/hpcdrive.html
Configuring your bash shell environment
If editing your bashrc -- open two terminals in biowulf. If you misconfigure your .bashrc, you will not be able to log into biowulf. Having two terminals open allows you to fix anything that errors out.
Edit .bashrc file in your home drive
umask 002 #Gives automatic group permissions to every file you create -- very very helpful for working with your team #Add modules bin path to access the MEG modules PATH=/data/MEGmodules/bin:$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
#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