Code Orange
All publicly available lab-wide software is stored and updated on our GitHub page. This section of our website merely serves to introduce some highlights. GitHub and OSF links associated with specific manuscripts are featured from the lab’s publications section, as well as in the articles themselves.
Though we try to keep functions documented wherever possible, if any issues arise with implementation, we’ll do the best we can to respond to questions and feedback.
If you use tools from the lab, please cite the relevant GitHub or OSF repository and any related publications.
iEye
MATLAB toolbox for interactive display and automatic analysis of eye-tracking data from memory-guided saccade experiments.
Interactive version (used in Mackey et al, 2016a; 2016b; Mackey & Curtis 2017): [GitHub]
Automated scoring (active development, currently in use): [GitHub]
Documentation available in most functions, in addition to README on GitHub.
fMRI preprocessing & analysis
AFNI scripts for preprocessing multiband fMRI data. Procedures will be described in detail in forthcoming preprints and publications.
Data processing involves: (1) surface reconstruction from T1 & T2 high-resolution anatomical images using Freesurfer, (2) standard spatial preprocessing steps (unwarping, motion correction, registration to anatomical images, surface smoothing, projection into volume space) using AFNI, (3) standard temporal normalization steps (linear detrending, conversion to percent signal change per voxel) using AFNI, and (4) additional custom processing, including computation of receptive field model parameters and multivariate analyses, using custom MATLAB and Python scripts, detailed below:
Preprocessing scripts: [GitHub] (requires Freesurfer 6.0, AFNI, vistasoft)
Utility functions for extracting timeseries from nii files, etc (MATLAB): [GitHub]
Tools for GPU accelerating large-scale linear regression problems (e.g., ‘grid fits’): [GitHub] (requires CUDA-compatible NVidia GPU and Windows or Linux computer)
Custom version of vistalab’s vistasoft package for GPU-accelerated RF model fitting: [GitHub] (requires [gridfitgpu])
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Currently under development: Python module to perform model-fitting directly on subject’s native surface
Stimulus presentation
Scripts for stimulus presentation used across studies (typically, using Psychtoolbox)
Attended bar task used for voxel receptive field modeling and retinotopic mapping: [GitHub]