mshvartsman / SRM

Shared Response Model (SRM) of NIPS 2015

Shared Response Model (SRM)

Library for Shared Response Model, related methods and experiment pipelines

Developed by Cameron PH Chen @ Princeton (https://cameronphchen.github.io)

If you only want to use SRM on your dataset, checkout Use_SRM

Paper:

If you use this code or SRM in scientific publication, citing the following paper is appreciated:

A Reduced-Dimension fMRI Shared Response Model

Po-Hsuan Chen, Janice Chen, Yaara Yeshurun, Uri Hasson, James V. Haxby, Peter J. Ramadge Advances in Neural Information Processing Systems (NIPS), 2015. Paper

Bibtex:

@inproceedings{phchen2015srm,
  title={A Reduced-Dimension f{MRI} Shared Response Model},
  author={Chen, Po-Hsuan and Chen, Janice and Yeshurun, Yaara and Hasson, Uri and Haxby, James V. and Ramadge, Peter J. },
  year={2015},
  booktitle={Advances in Neural Information Processing Systems (NIPS) },
}

To use the code and data please do

# clone code
git clone https://github.com/cameronphchen/SRM.git
# clone data (make sure git-lfs is installed on your machine https://git-lfs.github.com/)
git lfs pull

##Code Structure:

Please refer to code/readme.txt for procedure to replicate NIPS results

1. SRM/code:

• alignment_algo : alignmetn algorithms
• experiments : experiments, called by run_exp*.py
• plot : pipelines for aggregating results and generating figures
• preprocessing : preprocessing procedure for each dataset
• sh_script : shell script for running experiments in batch
• test : testing
• transform_matrix : code to match up the testing subject after having template
• run_exp_imgtrn_mysseg.py : experiment code for training on image testing on mystery segment
• run_exp_noLR_idvclas.py : experiment code for group classification
• run_exp_noLR.py : experiment code for image prediction and myster segment identification without seperating left and right hemisphere
• run_exp.py : experiment code for image prediction and myster segment identification seperating left and right hemisphere

2. SRM/data:

• In data folder, there should be data/input, data/working, data/output

##Datasets :

• raider : .mat files in data/input/raider/. If you use this dataset please refer to Haxby et at. 2011 Neuron.

• forrest: Please refer to www.studyforrest.org for forrest dataset

• sherlock and audiobook: The papers for these two datasets are still under review, so the datasets are not available at this point.