Normally, if you wanted to run something in EEGLAB, you start up MATLAB on Hoffman2, wait for a node to check out, wait for a license, and then start crunching numbers.
But what if your analysis in EEGLAB is going to take 10 hours, and you need to shut your computer down and leave in five hours? Or you don't want your MATLAB job to crash just because your flaky WiFi decides to die in hour nine of the analysis?
Well, if you have run this analysis before and have the "EEG.history" contents, you should be able to create a MATLAB script (*.m file) from said history and run it as a headless job on Hoffman2.
|Learn how to submit command line scripts and feel powerful controlling lots of computers||Have to learn command line scripts and how to submit jobs correctly|
|Be able to have your analysis run without tying up your computer for hours or days at a time||Have to run the analysis through at least once partially to create your script|
|Be able to run MATLAB jobs longer than 24 hours||Have to be comfortable editing MATLAB code to create your *.m file|
|Be able to run MATLAB jobs that use way more memory than your laptop can.|
|Possibly be able to run multiple analyses at once if you make the extra step and compile your code (so it doesn't need a MATLAB license)|
If you think the Pros outweigh the Cons, and they certainly do if you are processing more than one subject, then this is the solution for you.
If you know the exact commands you need to run, or have the contents of an "EEG.history" from a previous analysis, then the general *.m file to create will be the the following example, found at
% eeglab_example_job.m % % Edward Lau % eplau[at]ucla[dot]edu % 2014.03.06 % Example EEGLAB script that can be submitted as a job on Hoffman2. % % This M-file will: % 0. Set the paths for the input and output files. % 1. Load the EEGLAB "set" file % 2. Bandpass filter it to 1-45Hz % 3. Average re-reference the data % 4. Save the new data file with "preproc" appended to the old name (e.g. worked on "Subj1.set" resulting in "Subj1_preproc.set) % % % WARNING: % This example does not necessarily reflect the best practices for how EEG should be pre-processed and % should only be viewed as an example of how to script basic EEGLAB steps. %% 0. Variables to set % The directory where the data to be processed lives. INPUT_DIR = '/u/home/FMRI/apps/eeglab/current/sample_data/'; % The EEGLAB ".set" file that should be processed INPUT_FILE = 'eeglab_data.set'; % The directory where the processed data should be saved OUTPUT_DIR = getenv('SCRATCH'); % The EEGLAB ".set" filename that should be saved after processing OUTPUT_FILE = sprintf('%s_%s.%s', INPUT_FILE(1:end-4), 'preproc', 'set'); %% Make sure EEGLAB is in your PATH, change "current" to whichever version of EEGLAB you prefer addpath(genpath('/u/home/FMRI/apps/eeglab/current')); %% Load up EEGLAB in headless mode eeglab('nogui'); %% 1. Load up your data EEG = pop_loadset('filename', INPUT_FILE, 'filepath', INPUT_DIR); % Set EEG variables appropriately EEG = eeg_checkset( EEG ); ALLEEG = EEG; CURRENTSET = 1; %% Do your analyses % This could be built from the contents of an EEG.history array from a previous analysis % 2. Bandpass filter 1-45Hz EEG = pop_eegfiltnew(EEG, 1, 45, 424, 0, , 0); EEG = eeg_checkset( EEG ); % 3. Average re-reference the data EEG = pop_reref( EEG, ); EEG = eeg_checkset( EEG ); %% 4. Don't forget to save your data afterward OUTDIR = getenv('SCRATCH'); EEG = pop_saveset( EEG, 'filename', OUTPUT_FILE, 'filepath', OUTPUT_DIR); EEG = eeg_checkset( EEG );