CONN : functional connectivity toolbox News

Online CONN 2024 workshop registration open

Alfonso Nieto-Castanon — Tue, 13 Feb 2024 3:31:14 GMT

We are pleased to announce that registration for the CONN 2024 functional connectivity workshop is now open. This workshop will take place ONLINE over ten consecutive Fridays with weekly 3-½ hour classes from 11am to 2:30pm EDT (UTC−04:00), starting on Friday April 5 and ending on Friday June 7 2024 (see https://courses.conn-toolbox.org/course-schedule for the course schedule details).

The CONN toolbox workshop offers intensive hands-on and highly interactive courses covering all aspects of functional connectivity analyses in CONN, and both beginners and advanced users are welcome. Classes take place over Zoom on Fridays for ten consecutive weeks. Zoom meetings of each class are recorded and made available to students to view at any time during the course. There are also practice homework assignments, and faculty is available during office-hour segments for additional student questions or support.

For additional information and registration see https://courses.conn-toolbox.org

Thank you for your support!
Alfonso Nieto-Castanon

Online CONN 2023 workshop starting soon

Alfonso Nieto-Castanon — Thu, 09 Nov 2023 10:01:56 GMT

We are pleased to announce that the CONN 2023 functional connectivity workshop will be starting in a couple of weeks, and there is still time to subscribe if you are interested. This workshop will take place ONLINE over five consecutive Mondays from 9am to 5pm EST (UTC−05:00), starting on Monday Nov 20 and ending on Monday Dec 18 2023.

The CONN toolbox workshop (https://www.conn-toolbox.org/workshops) offers intensive hands-on and highly interactive courses covering all aspects of functional connectivity analyses in CONN, and both beginners and advanced users are welcome. Classes will take place over Zoom on Mondays for five consecutive weeks, and there will be a bit of homework between consecutive weeks and office hours available to help with that.

For additional information and registration see https://education.martinos.org/home/using-the-conn-toolbox-for-functional-connectivity-analysis/
(and also see https://www.martinos.org/education/ for other great seminars and courses from the Martinos Center)

Best
Alfonso

CONN new release

Alfonso Nieto-Castanon — Wed, 15 Mar 2023 2:14:25 GMT

After a year in the making we are happy to announce the latest release of CONN (22a)!

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 (https://afni.nimh.nih.gov/pub/dist/doc/misc/instacorr.pdf) but across all subjects in a study (see 2nd-level fc-MVPA summary tab), new automated "Methods" descriptions (https://web.conn-toolbox.org/resources/citing-conn) 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 other additions and improvements.

See the release changes log (https://www.nitrc.org/frs/shownotes.php?release_id=4786) and the updated manual (https://web.conn-toolbox.org/resources/documentation/manual) for details.

We are also happy to announce some of our latest manuscripts describing QC procedures using CONN:
Morfini, F., Whitfield-Gabrieli, S., & Nieto-Castanon, A. (2023). Functional connectivity MRI Quality Control procedures in CONN. Frontiers in Neuroscience, 17:1092125. https://doi.org/10.3389/fnins.2023.1092125

and fc-MVPA analyses:
Nieto-Castanon, A. (2022). Brain-wide connectome inferences using functional connectivity MultiVariate Pattern Analyses (fc- MVPA). PLoS Comput Biol 18(11): e1010634. https://doi.org/10.1371/journal.pcbi.1010634

As always, please send us your feedback/comments/suggestions through the NITRC CONN forum (https://www.nitrc.org/forum/forum.php?fo...) and thank you all for your continuing support!

CONN new release

Alfonso Nieto-Castanon — Tue, 18 Feb 2020 1:59:35 GMT

We are happy to announce the latest release of CONN (19b).

This latest release brings a novel implementation of Threshold Free Cluster Enhancement (Smith & Nichols 2009) that can be used for voxel-based, surface-based, as well as ROI-to-ROI second-level analyses, increased compatibility with fMRIPrep preprocessing pipeline, new methods for cluster-based inferences for ROI-to-ROI connectivity matrices such as Functional Network Connectivity (Jafri et al. 2008) and Spatial Pairwise Clustering (Zalesky et al. 2012), the ability to define and estimate hierarchical multi-level models, and many other smaller fixes and improvements.

We are also happy to announce our new handbook with an updated description of all fMRI methods in CONN, which can be read or downloaded from https://www.conn-toolbox.org/fmri-methods .

As always, please send us your feedback/comments/suggestions through the NITRC CONN forum (https://www.nitrc.org/forum/forum.php?fo...) and thank you all for your continuing support!

New CONN release and tutorials

Alfonso Nieto-Castanon — Tue, 27 Jun 2017 1:00:14 GMT

We are happy to announce the latest release of CONN (17f). If you have not had the chance to update CONN recently this is a great time to do so and see what is all the fuzz about the new Quality Assurance plots and measures, increasing BIDS-compatibility support, and stability/usability improvements in distributed cluster or multi-processor environments.

We are also happy to announce the new site http://www.conn-toolbox.org where you can find video tutorials as well as detailed installation and configuration tips.

Last but not least, we are compiling a list of example CONN configuration instructions for several representative cluster computing environments, so if you have CONN installed in a distributed cluster, HPC, or multi-processor environment, and would like to contribute, please send us a description and/or your conn_jobmanager.mat file configuration details and help share the joy of distributed computations.

As always, please send us your feedback/comments/suggestions through the NITRC CONN forum (https://www.nitrc.org/forum/forum.php?forum_id=1144) and thank you all for your continuing support!

CONN New Year News

Alfonso Nieto-Castanon — Thu, 12 Jan 2017 2:16:03 GMT

Happy new year to all CONN users (CONNers?) out there!

A couple of quick news:

1) we are in the process of applying for a software development and maintenance grant for CONN. We need to show some measures of impact, so if you would like to contribute by writing a letter of support, mainly stating how you are using or have used CONN, and how it may have helped in your research, that would be hugely appreciated. If you are interested drop me a line at alfnie@gmail.com, we can send you the info and/or a letter of support template if that would make things simpler.

2) the 2017 CONN workshop is schedule to happen in Boston in May 1-5 (see http://www.nmr.mgh.harvard.edu/Learning_The_CONN_Toolbox for additional details). We have about half of the vacancies already reserved/registered, so if you are thinking about participating early registration is strongly recommended. This is typically a great opportunity to learn everything there is to know about CONN and also get to interact with the team and other CONN users, so everybody from novice to experts are welcome (we might even hand out CONNvert certificates at the end!)

Best regards and happy new year again!
Alfonso

CONN new release (15f)

Alfonso Nieto-Castanon — Fri, 25 Sep 2015 12:56:50 GMT

We are happy to announce the latest release of CONN (release 2015f).

Among several improvements and new features we would like to highlight the ability to massively parallelize your functional connectivity analyses by running CONN in a computer cluster distributed environment. Grid and cloud computing environments are becoming increasingly ubiquitous in research, and many institutions already offer researchers readily access to cluster computing resources. CONN allows you to take advantage of this by offering a user-friendly way to use these resources. All of the functional/anatomical Preprocessing steps (e.g. realignment, slice-timing correction, normalization, etc.), Setup, Denoising, and first-level Analyses in CONN can now be executed in parallel (as much as one separate process per subject), allowing you to analyze hundreds of subjects in the time it would typically take to process just one or a few subjects. CONN offers native support for some of the most common grid schedulers (Grid Engine, PBS/Torque, LSF) and simple options to accomodate other schedulers/environments.

If your institution offers a computer cluster environment we encourage you to give this new functionality a try. In most cases there should be zero configuration required, just select your institution scheduler-type and decide how many parallel jobs you would like your processing step to be broken into. Parallelization functionality can be used from the CONN gui as well as through batch scripts. If your institution does not offer Matlab access or if you are using a third-party cloud computing environment (e.g. AWS, NITRC-CE) we will be offering shortly pre-compiled versions of CONN that do not require a Matlab license/environment. To get started see the CONN gui Help.Documentation.GridComputing and Tools.GridComputing menus (and for batch scripting see conn_batch batch.parallel field)

Hope this helps!
CONN team

Announcing Cincinnati CONN course (MGH/HST)

Alfonso Nieto-Castanon — Tue, 09 Jun 2015 12:46:21 GMT

We are pleased to announce a three day intensive software training workshop in Cincinnati this summer, July 20-22 2015, on the use of the CONN Toolbox.

The course welcomes both new and existing users of CONN. It will cover basic and advanced features of CONN as well as general topics in functional connectivity analyses. The course faculty will include Susan Whitfield-Gabrieli, Alfonso Nieto-Castanon, Sheeba Arnold Anteraper, and Robert L. Savoy.

Details can be seen at http://www.martinos.org/CONN_in_Cincinnati

Please note that number of attendees is highly limited so early planning and registration is recommended.

CONN v.13n Released

Alfonso Nieto-Castanon — Mon, 08 Jul 2013 6:56:10 GMT

The latest revision of the CONN functional connectivity toolbox (v.13n) includes some interesting additions we would like to highlight:

1) Network based statistics (NBS). ROI-to-ROI second-level analyses now include the ability to use NBS to control for false positives at the family-wise level, which is particularly useful when analyzing the entire functional connectome. NBS is a great method proposed by Zalesky et al. (Zalesky, A., Fornito, A., Bullmore, E.T. 2010. Network-based statistic: Identifying differences in brain networks. NeuroImage, 53(4):1197-1207) that controls for family-wise error (FWE) in mass-univariate testing of a full ROI-to-ROI connectivity matrix. It is a non-parametric approach based on permutation tests that looks at the extent of interconnected effects when analyzing the ROI-to-ROI connectivity matrix.
We have integrated and adapted their original implementation (which you can find, and we highly recommend, at www.nitrc.org/projects/nbs) to work with any mixed within- and between- subjects design that the CONN toolbox allows, using a general permutation of residuals approach (Still, A. W. and White, A. P., 1981. The approximate randomization test as an alternative to the F test in analysis of variance. Br. J. Math. Stat. Psychol., 34, 243–252) that requires minimal user interaction. In addition to network-level corrections, we have also added similar seed-level corrections to give users additional options for family-wise error control when analyzing the entire connectome or when looking at multiple seeds simultaneously. We will be updating the manuals soon to detail the new options but in the meantime you can find more details about these in the FAQ (http://www.alfnie.com/software/conn#TOC-Results:-What-are-NBS-connection--seed--and-network--level-statistics-in-ROI-to-ROI-analyses-and-how-to-use-them-)

2) There has been some recent and interesting discussion regarding the influence of some methodological choices during nuisance regression of physiological/movement effects in fcMRI (Hallquist, M.N., Hwang, K., Luna, B., 2013. The nuisance of nuisance regression: Spectral misspecification in a common approach to resting-state fMRI preprocessing reintroduces noise and obscures functional connectivity. NeuroImage, 82:208-225). This manuscript highlights how a somewhat common preprocessing pipeline (referred as BPreg; band-pass before regression) that applies temporal band-pass filtering to the BOLD signal timeseries before removing nuisance effects can lead to inappropriate control of physiological/movement effects. The CONN toolbox uses instead by default a procedure referred as RegBP (regression before band-pass), which the manuscript finds to have similar performance to their preferred method (referred as Simult; simultaneous regression and band-pass). While the differences between these two methods (RegBP and Simult) seem to be relatively minor, with perhaps slightly better control offered by the 'Simult' approach at the cost of perhaps lower specificity, we have now included both methods as options in the Preprocessing tab, and encourage users to try these out. We expect that the 'Simult' approach should offer better control in those cases where the nuisance regressors (e.g. estimated subject motion parameters) and the associated BOLD signal effects (e.g. movement-related artifacts) show different spectral characteristics, e.g. when their relation is best characterized as a non-zero-order filtering operation; but it could be suboptimal -not the minimum variance estimator, leading to lower sensitivity yet still valid results- if they show similar spectral characteristics, e.g. when their relation is best characterized as a purely zero-order linear operation. We have left for now RegBP as the default settings in the toolbox just for consistency with previous versions of the toolbox, but we will keep a close tab on this issue and update the default settings if the community consensus seems to lean towards a different option.

Last there are as usual a few other smaller additions such as bug fixes (thanks to Vincent Beliveau for suggesting an effective solution to the svd-convergence issue that appeared under some Matlab versions!) and other minor modifications (we have finally added an option for the users to modify the default GUI font size -under Help->GUI settings-, which seemed to be a popular request; we have also further customized and extended the new 'Connectome view' display in the ROI-to-ROI results gui). We hope you find these useful as well, and as always please feel free to post your questions/issues/thoughts/suggestions in the forum, and thank you all for your support!.

conn toolbox version 13 released

Alfonso Nieto-Castanon — Mon, 31 Oct 2011 3:56:32 GMT

We are happy to announce the release of the latest version of the connectivity toolbox (conn v.13)

Some of the most notable additions to the toolbox include:

* New second-level analysis options for F-contrast and multivariate statistics for voxel-level and ROI-level analyses
* New voxel-to-voxel analyses for exploring the entire (whole-brain) connectome
* Additional graph-theory measures for exploring the properties of ROI-to-ROI networks
* Optimizations to increase the speed and reduce the storage requirements for many of the analyses, as well as greater flexibility to define the desired analyses and output files
* New output display options including 3d renderings of voxel-level and ROI-level results

There are also many minor additions, such as improvement to the graphical user interface, increased flexibility to resample voxel-level analyses to the desired resolution, support for sparse acquisition, support for topological-FDR corrections in voxel-level analyses, addition of slice-timing correction to the spatial preprocessing pipeline, and many others. We hope you enjoy the new version and please let us know through the forum if you find any issues or have any questions/feedback/suggestions