CONN

functional connectivity toolbox

80,000 lines of code

50,000 downloads   

yearly software releases since 2012

@ nitrc.org/projects/conn 


6,000 studies

academic publications using CONN for functional connectivity analyses

@ google scholar

5,000 registered users

14,000 forum posts 

support forum for CONN users

@ nitrc.org/projects/conn 

Latest news

CONN workshops offer 35 hours of intensive hands-on and highly interactive classes covering all aspects of functional connectivity analyses in CONN. Next workshop will take place online between Sept 16 and Oct 18 (Fall 2024 online workshop). Places are limited, consider registering early to guarantee a seat. Thank you for your support!

This release brings many exciting updates, including new options for fc-MVPA analyses and an interactive GUI exploring the entire brain-wide functional connectome (similar to AFNI InstaCorr but combining all subjects in a study; see 2nd-level fc-MVPA summary tab), new automated "Methods" descriptions to help describe CONN's processing and analysis steps in your manuscripts, and several new displays options (e.g. 'connections display' and 'glass display' in ROI-to-ROI, or  'network display' in voxel-level results explorer windows), among many others. See the release changes log and the updated manual for details.

Many replicability efforts stumble  at the initial steps by a lack of rigorous reporting of the specific choices used by a team when processing and analyzing their data. To help change this, CONN can now create boilerplate descriptions of the specific preprocessing, denoising, and analysis choices that were used in your CONN project.  These automatic descriptions are distributed under a public domain license and can be used, copied, modified and redistributed freely as part of the Methods section of your manuscript, or anywhere else. See this section for additional details. 

This is a work in progress and we welcome your feedback to help us make these descriptions as informative and useful as possible!

Methods.pdf

Fc-MVPA analyses allow researchers to test hypotheses about the entire functional connectome (all voxel-to-voxel functional connections across the entire brain), without having to limit the analyses to a single or a few seed areas (e.g. SBC analyses) or a specific parcellation of the brain into ROIs (e.g. RRC analyses). For example, questions like "is functional connectivity different between patients and control subjects?",  "does functional connectivity change with an intervention?", or "what aspects of functional connectivity covary with symptom severity?" can be asked using fc-MVPA examining the entire set of (billions of) functional connections between all pairs of individual voxels in the fMRI images.  

Software description

CONN is an OPEN-SOURCE SPM-based cross-platform software for the computation, display, and analysis of functional connectivity Magnetic Resonance Imaging (fcMRI). CONN is used to analyze resting state data (rsfMRI) as well as task-related designs. Processing and analysis steps in CONN include:

When used within a distributed cluster or multi-processor environment CONN can automatically parallelize most time consuming steps in the fcMRI processing pipeline, allowing the analyses of hundreds of subjects in minimal time. CONN can be entirely controlled through a user-friendly GUI, or through batch scripts/commands. 

The toolbox is developed in Matlab, and it is distributed both as Matlab source code and as a pre-compiled executable file (standalone release, no Matlab installations or licenses required).

See the fMRI methods section for a detailed description of all processing and analysis methods available in CONN.

Citing CONN

See the section citing CONN for details about the automatically-generated boilerplate text describing the procedures and methods used by CONN on your specific project, including proper attribution to the different software and methods used

To cite CONN in your work, please include CONN's RRID and at least one of the following general references:

e.g. we used CONN (RRID:SCR_009550) [1] for the analysis of fMRI data.

To cite one specific version of CONN in your work, please include the specific DOI of your CONN release/version:

e.g. Functional images were preprocessed and denoised using the default options in CONN version 22a [2]. 


(note: doi's for older versions of CONN)

for CONN22a : [2] Nieto-Castanon, A., & Whitfield-Gabrieli, S. (2022). CONN functional connectivity toolbox: RRID SCR_009550 release 22. Boston, MA. doi:10.56441/hilbertpress.2246.5840

for CONN21a : [2] Nieto-Castanon, A., & Whitfield-Gabrieli, S. (2021). CONN functional connectivity toolbox: RRID SCR_009550 release 21. Boston, MA. doi:10.56441/hilbertpress.2161.7292

for CONN20b : [2] Nieto-Castanon, A., & Whitfield-Gabrieli, S. (2020). CONN functional connectivity toolbox: RRID SCR_009550 release 20. Boston, MA. doi:10.56441/hilbertpress.2048.3738

for CONN19c : [2] Nieto-Castanon, A., & Whitfield-Gabrieli, S. (2019). CONN functional connectivity toolbox: RRID SCR_009550 release 19. Boston, MA. doi:10.56441/hilbertpress.1927.9364

for CONN18b : [2] Nieto-Castanon, A., & Whitfield-Gabrieli, S. (2018). CONN functional connectivity toolbox: RRID SCR_009550 release 18. Boston, MA. doi:10.56441/hilbertpress.1818.9585

for CONN17f : [2] Nieto-Castanon, A., & Whitfield-Gabrieli, S. (2017). CONN functional connectivity toolbox: RRID SCR_009550 release 17. Boston, MA. doi:10.56441/hilbertpress.1744.6736

for CONN12p : [2] Nieto-Castanon, A., & Whitfield-Gabrieli, S. (2012). CONN functional connectivity toolbox: RRID SCR_009550 release 12. Boston, MA. doi:10.56441/hilbertpress.1243.7679

for CONN9 : [2] Nieto-Castanon, A. & Whitfield-Gabrieli, S. (2009). CONN functional connectivity toolbox: RRID SCR_009550 release 9. Boston, MA. doi:10.56441/hilbertpress.0984.0411