NIH_MEG_Workshop_AdvancedTopics

Calendar
Biowulf Setup
Install

Day 1 (05/02/2025) - FAES ROOM 6 – B1C208

Connectivity and Decoding

Time	Topic	Presenter
9:00 - 9:15	Computer Setup etc
9:15 - 9:30	Course Intro + Souce Localization (for connectivity)	Jeff
9:30 - 10:30	Connectivity Background	Lucrezia
10:30 - 11:30	Connectivity Code
11:30 - 12:30	Lunch
12:30 - 1:30	Decoding Background	Lina
1:45 - 2:30	Decoding Applications	Shruti, Alexis, Sebastian
2:30 - 4:00	Decoding Code

Computer Setup Using NoMachine

Once in NoMachine on Biowulf, copy the following lines into your terminal. Start a processing terminal

sinteractive --mem=32G --cpus-per-task=12 --tunnel  #Wait for this to start

module use --append /data/MEGmodules/modulefiles  #You can add this to your .bashrc for convenience
module load meg_workshop/2025adv.1

get_code   #Copy the code to your current directory
get_data   #Copy and untar the data to your /data/${USER}/meg_data_workshop

cd /data/${USER}/NIH_MEG_Workshop_AdvancedTopics
jupyter notebook --no-browser --port $PORT1

Once the prompts come up, you will see a line like the following:

Open an Internet Browser in the top left corner and add the IP address and token into the address bar

Alternative version using SSH Tunnels (This is more difficult to setup, but faster to use)

Log into biowulf: ssh -Y USERNAME@biowulf.nih.gov

#You can type tmux before starting sinteractive to have a persistent session between disconnecting wifi
#Allocate resources for processing
sinteractive --mem=32G --cpus-per-task=12 --gres=lscratch:10 --tunnel --time=08:00:00

You will see a line like the below. Follow the instructions (start a new terminal into biowulf), then return to original terminal for the rest of the commands.

Copy the following lines into your terminal. This will copy the code/notebooks and data into your local folder.

sinteractive --mem=32G --cpus-per-task=12 --tunnel  #Wait for this to start

module use --append /data/MEGmodules/modulefiles  #You can add this to your .bashrc for convenience
module load meg_workshop/2025adv.1

get_code   #Copy the code to your current directory
get_data   #Copy and untar the data to your /data/${USER}/meg_data_workshop

cd /data/${USER}/NIH_MEG_Workshop_AdvancedTopics
jupyter notebook --no-browser --port $PORT1

Enter this into the address bar of your web browser localhost:<PORT>

NOTE:If you get something about a token: Copy it from the commandline

Optional: Install Code (on your own system)

Install using make:
make install_env
Install from conda environment.yml file:
conda env create --name envname --file=environments.yml