software

CONN: fMRI functional connectivity toolbox

The Gabrieli Lab, McGovern Institute for Brain Research. Massachusetts Institute of Technology

Matlab toolbox for performing functional connectivity analyses of fMRI data. Features: ROI-to-ROI, seed-to-voxel, voxel-to-voxel (whole brain connectome), and graph-theory analyses; resting state (rsfcMRI) as well as task-related connectivity analyses; gui and batch processing. Methods: Spatial preprocessing; CompCor method for removing physiological and other confounds; first-level univariate and multivariate regression and bivariate and semipartial correlation connectivity measures; second level mixed within- between- subjects random effect analyses.

Visit conn-toolbox.org for more details or conn NITRC site to download this software

Users are welcome to post their questions/comments at the conn toolbox public forum (NITRC login required)

rtart: Real-time articulatory synthesizer

SpeechLab, Cognitive and Neural Systems Department. Boston University

Low-dimensional articulatory speech synthesizer that users can control in real-time using mouse movements

Visit the Speechlab BU site for more information

design_efficiency: analysis of subject-level experimental design efficiency for fMRI studies

SpeechLab, Cognitive and Neural Systems Department. Boston University

Design efficiency computation for block- or event- related design. It supports continuous and sparse acquisition sequences, and arbitrary first-level contrasts. It includes a simple GUI for inspection of the effect of variable choices of common design parameters

Download software @ github

EL: command-line fMRI pipeline for subject-centric task-activation analyses

EvLab, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology

A preprocessing and analysis pipeline that combines CONN preprocessing and denoising steps (e.g. scrubbing, aCompCor), SPM first-level task-activation analyses (including block-designs, event-related designs, and parametric modulation analyses), and including options for SPM_SS localizer and subject-specific analyses.

Visit EvLab MIT site for more information

FL: command-line fMRI pipeline for group-centric task-activation analyses

SpeechLab, Cognitive and Neural Systems Department. Boston University

A preprocessing and analysis pipeline that combines a BIDS-compatible data organization, CONN preprocessing and denoising steps, SPM first-level task-activation analyses, and General Linear Model group-level analysis, including options for parametric (RFT) and non-parametric (randomization/permutation) statistics and inferences, TFCE, as well as surface- and ROI- level analyses.

Visit Speechlab BU site for more information

DIVA: simulink Matlab model

SpeechLab, Cognitive and Neural Systems Department. Boston University

Simulink implementation of DIVA speech production model (Guenther et al. 2006)

Visit the Speechlab BU site for more information

spm_ss: fMRI functional localizers, subject-specific analyses

Kanwisher Lab, McGovern Institute for Brain Research. Massachusetts Institute of Technology

Matlab SPM-toolbox for performing second-level analyses of functional MRI data using subject-specific functional localizers to identify the voxels/regions of interest. The toolbox implements ROI-level and voxel-level analyses, and it implements an automatic cross-validation procedure when the localizers are not orthogonal to the effects-of-interest. ROI-level analyses allow manually defined parcels of interest, as well as automatically-defined ones (GcSS procedure, Fedorenko et al. 2010). General linear model second-level analyses are implemented, including ReML and OLS estimation of population level effects. Hypothesis testing includes standard univariate tests as well as multivariate tests for mixed within- and between-subject designs (T, F, and Wilks' lambda statistics)

Visit the spm_ss NITRC site for more information and downloading this software

ART: Artifact Detection Toolbox (role: contributor)

The Gabrieli Lab, McGovern Institute for Brain Research. Massachusetts Institute of Technology

Matlab toolbox for post-processing fMRI data. Includes software for comprehensive analysis of sources of artifacts in timeseries data including spiking and motion. Most compatible with SPM processing, but adaptable for FSL as well.

Visit the art NITRC site for more information and downloading this software

spm_crossvalidation: fMRI cross-validation tools

The Gabrieli Lab, McGovern Institute for Brain Research. Massachusetts Institute of Technology

Matlab SPM-based tools for extracting cross-validated data from functional ROIs. Works in conjunction with the standard SPM second-level results window. Re-evaluates second-level analyses and contrast leaving one subject out at a time (leave-one-out cross-validation), and extracts subject-specific effect size estimates from the conjunction of supra-threshold voxels and one or multiple a-priori defined ROIs.

Download software @ github

REX: Region-of-interest extraction toobox

The Gabrieli Lab, McGovern Institute for Brain Research. Massachusetts Institute of Technology

Matlab toolbox for extraction of image values and time series from single voxels, voxel clusters and cluster collections. Data extraction features flexible ROI definition (including single- and multiple-ROI nifti volumes), global and ROI-specific scaling options, and descriptive statistics from clusters of voxels including mean, median, voxel-weighted mean, and multiple eigenvariates. In addition to data extraction the rex toolbox performs ROI-based analyses of functional data complementing SPM voxel-based analyses.

Download software @ NITRC

XKCD Megan Simulator

Procedural art: a user-friendly GUI allows users to control Megan's movements, visualize the results in real-time, and create snapshots and videos. A variety of predefined (and somewhat silly) environments will have Megan dancing, jumping, painting, skating, and more.

Download software @ MathWorks FileExchange