conn: fMRI functional connectivity toolbox (role: developer; status: active)
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 user resources and recent articles using this toolbox, or the conn FAQ section for frequently asked questions
  Visit the 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 (role: developer; status: under development)

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 CNS site for more information
   
 
 
 
 
 
 
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
  
   
 

 
 
 
DIVA: simulink Matlab model (role: developer)

SpeechLab, Cognitive and Neural Systems Department. Boston University

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

  Visit the Speechlab CNS site for more information

   
 
 
 
 
 
 
spm_ss: fMRI functional localizers, subject-specific analyses (role: developer)
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
 
   
 
 

   
 
 
spm_crossvalidation: fMRI cross-validation tools (role: developer)
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 here* 
   
 
 
 
 
 
rex: Region-of-interest extraction toobox (role: developer)

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 here*

 

   
 
 
 
 
   
 

 
 
 
 
 
   
 
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 
 
* MIT software is distributed under the MIT/X Consortium License (http://www.opensource.org/licenses/mit-license.php)