DynaConn

Dynamic Functional Connectivity (DynaConn) Graphical User Interface (GUI) Toolbox for fMRI.
With this toolbox, you can do dynamic sliding time-window analyses of fMRI datasets.

It is MATLAB-based, so you need MATLAB. It should work with any version of MATLAB that is installed 2013 or later. It uses some, mostly modified, SPM8 functions, but those are already bundled in it so you do not have to download SPM8 separately.
It also works with GIFT ICA results; i.e. once you run ICA with GIFT, you can do dynamic F(N)C analysis of the IC time-courses. We call it DFNC since there are IC "networks" that you are analyzing.
You can find and download the toolbox on bitbucket here:
https://bitbucket.org/johnesquivel/dynaconn.git  
Check out the User's Guide/Manual (pdf) and the short videos here in order to have a quick idea of its capabilities.  

Please contact Dr. Sakoglu (sakoglu[at]uhcl[dot]edu) if you download it and for any questions and comments.

Collaborators: Dr. Mutlu Mete, Associate Professor; and John E. Esquivel, MS Student, TAMUC Computer Science Department.

If you download DynaConn & use it for your analysis, please cite the following work:
(Visit https://www.drsakoglu.com/p/publications.html for links to full text of these publications)
On the DynaConn toolbox:
 John Esquivel, Mutlu Mete, Unal Sakoglu, “DynaConn: A Software for Analyzing Brain’s Dynamic Functional Connectivity from fMRI Data,” Midsouth Computational Biology and Bioinformatics Society Conference (MCBIOS), March 2014, Stillwater, OK.
 John Esquivel, Mutlu Mete, Unal Sakoglu, “Software for Analyzing Brain’s Dynamic Functional Connectivity from fMRI,” Proc. IEEE EMBS Annual Medical Device Symposium, November 2013, Dallas, TX.
 On the sliding-window DFC methodology:
 Unal Sakoglu, Geoffrey D Pearlson GD, Kent A Kiehl, Yongmei M Wang, Andrew M Michael, Vince D Calhoun, “A Method for Evaluating Dynamic Functional Network Connectivity and Task-Modulation: Application to Schizophrenia,” Magnetic Resonance Materials in Physics, Biology and Medicine (MAGMA), Special Issue on MR Imaging of Brain Networks, Vol. 23, pp. 351-366 (2010). <-seminal/first paper on sliding-window DFC/DFNC
 Unal Sakoglu, Vince D Calhoun, “Temporal Dynamics of Functional Network Connectivity at Rest: A Comparison of Schizophrenia Patients and Healthy Controls,” 15^th Annual Meeting of the Organization for Human Brain Mapping, June 2009, San Francisco, CA. Another link to full text.  <-one of the seminal presentations of DFC

Unal Sakoglu, Andrew M Michael, Vince D Calhoun, “Classification of schizophrenia patients vs healthy controls with dynamic functional network connectivity,” Proc. 15^th Annual Meeting of the Organization for Human Brain Mapping, June 2009, San Francisco, CA. Another link to full text. <-one of the seminal presentations of DFC

Unal Sakoglu, Vince D Calhoun, “Functional network connectivity with temporal derivatives of sICA time-courses in schizophrenia patients vs healthy controls,” Proc. 17^th Annual Meeting of the International Society for Magnetic Resonance in Medicine, #3675, April 2009, Honolulu, HI. Link. <-one of the seminal presentations of DFC

Unal Sakoglu, Vince D Calhoun, “Dynamic windowing reveals task-modulation of functional connectivity in schizophrenia patients vs healthy controls,” Proc. 17^th Annual Meeting of the International Society for Magnetic Resonance in Medicine, #3676, April 2009, Honolulu, HI. <-one of the seminal presentations of DFC