Past, Present and Future of Open Science (Software/process demo): Group ICA Toolbox: New features and developments

[jsheunis]

Group ICA Toolbox: New features and developments

By Srinivas Rachakonda, Georgia State University
Collaborators: Dr. Vince Calhoun and Dr. Armin Iraji

• Theme: Past, Present and Future of Open Science
• Format: Software/process demo

Abstract

We provide a brief demo on the new features in the upcoming version of the Group ICA Toolbox (GroupICATv4.0c). The Group ICA toolbox (GIFT, EEGIFT and SBM) is a widely used and open MATLAB toolbox in the neuroimaging community for analyzing medical imaging data offering a wide variety of source separation techniques including independent component analysis and independent vector analysis. We specifically focus on three newer aspects of GIFT including the various options for using the tools stand-alone without a Matlab license (e.g. Docker, Nipype/giftpy and stand-alone executable), fully automated ICA using spatial references as priors or autolabelling and dynamic connectivity based toolboxes in both the spatial and temporal domains.

Useful Links

https://trendscenter.org/software/gift/
https://github.com/trendscenter/groupica_docker

Tagging @calhounlab

[calhounlab]

Thanks Stephan. Is there a place where i can enter the collaborators Dr. Vince Calhoun and Dr. Armin Iraji?

…

________________________________ From: Stephan Heunis <notifications@github.com> Sent: Friday, May 15, 2020 10:38 AM To: ohbm/osr2020 <osr2020@noreply.github.com> Cc: Naga Satya Kanaka Srinivas Rachakonda <srachakonda@gsu.edu>; Mention <mention@noreply.github.com> Subject: [ohbm/osr2020] Past, Present and Future of Open Science (Software/process demo): Group ICA Toolbox: New features and developments (#37) Group ICA Toolbox: New features and developments By Srinivas Rachakonda, Georgia State University * Theme: Past, Present and Future of Open Science * Format: Software/process demo Abstract We provide a brief demo on the new features in the upcoming version of the Group ICA Toolbox (GroupICATv4.0c). The Group ICA toolbox (GIFT, EEGIFT and SBM) is a widely used and open MATLAB toolbox in the neuroimaging community for analyzing medical imaging data offering a wide variety of source separation techniques including independent component analysis and independent vector analysis. We specifically focus on three newer aspects of GIFT including the various options for using the tools stand-alone without a Matlab license (e.g. Docker, Nipype/giftpy and stand-alone executable), fully automated ICA using spatial references as priors or autolabelling and dynamic connectivity based toolboxes in both the spatial and temporal domains. Useful Links https://trendscenter.org/software/gift/<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftrendscenter.org%2Fsoftware%2Fgift%2F&data=02%7C01%7Csrachakonda%40gsu.edu%7Cb9dc588eaae24e4ec0c208d7f8ee5633%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C637251574847350407&sdata=K4sxxu63bxe0jGuVgcJIZtZmCUatBgbtKUDQm8hxbeU%3D&reserved=0> https://github.com/trendscenter/groupica_docker<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftrendscenter%2Fgroupica_docker&data=02%7C01%7Csrachakonda%40gsu.edu%7Cb9dc588eaae24e4ec0c208d7f8ee5633%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C637251574847360396&sdata=n07j7%2BXfWRcomU7BXU0A2nQAWVtnDcNhemdwBJyA%2BWM%3D&reserved=0> Tagging @calhounlab<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fcalhounlab&data=02%7C01%7Csrachakonda%40gsu.edu%7Cb9dc588eaae24e4ec0c208d7f8ee5633%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C637251574847360396&sdata=PdN04AQ3lpYji7Lu3hmItu4zNnm6EXbY79FCDp6fYZY%3D&reserved=0> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fohbm%2Fosr2020%2Fissues%2F37&data=02%7C01%7Csrachakonda%40gsu.edu%7Cb9dc588eaae24e4ec0c208d7f8ee5633%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C637251574847360396&sdata=QweMdVu60ROGQAYaj3%2BAJBbUXHnJGsJwLa%2Byh97F3l0%3D&reserved=0>, or unsubscribe<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAIA5DQZ2YHQNDKJLHXUN7PLRRVVWVANCNFSM4NBW7VBQ&data=02%7C01%7Csrachakonda%40gsu.edu%7Cb9dc588eaae24e4ec0c208d7f8ee5633%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C637251574847370393&sdata=IwtjSFTXOAmLHCwZgygoqKtMIqw%2FWtZoQ%2FU33zmJLRg%3D&reserved=0>. CAUTION: This email was sent from someone outside of the university. Do not click links or open attachments unless you recognize the sender and know the content is safe.

[jsheunis]

I've added this at the top, is that fine?

[calhounlab]

Prefect. Thanks Stephan

…

________________________________ From: Stephan Heunis <notifications@github.com> Sent: Friday, May 15, 2020 2:17 PM To: ohbm/osr2020 <osr2020@noreply.github.com> Cc: Naga Satya Kanaka Srinivas Rachakonda <srachakonda@gsu.edu>; Mention <mention@noreply.github.com> Subject: Re: [ohbm/osr2020] Past, Present and Future of Open Science (Software/process demo): Group ICA Toolbox: New features and developments (#37) I've added this at the top, is that fine? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fohbm%2Fosr2020%2Fissues%2F37%23issuecomment-629461228&data=02%7C01%7Csrachakonda%40gsu.edu%7Cfb466ec342b74933ed6d08d7f90cf1ad%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C637251706308448196&sdata=o2l5DFGLpmD5OCePjtTfu09zg5fn80%2BM7vIzk%2FB3ktE%3D&reserved=0>, or unsubscribe<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAIA5DQ4IPKSAXEYMIMY25TTRRWPMHANCNFSM4NBW7VBQ&data=02%7C01%7Csrachakonda%40gsu.edu%7Cfb466ec342b74933ed6d08d7f90cf1ad%7C515ad73d8d5e4169895c9789dc742a70%7C0%7C0%7C637251706308453184&sdata=hHdIJgRghGxwUdP%2FbNEqKsC7yuGUNKgUICXhs%2Bxa76s%3D&reserved=0>. CAUTION: This email was sent from someone outside of the university. Do not click links or open attachments unless you recognize the sender and know the content is safe.

[pbellec]

GIFT is indeed a widely used toolbox. Having a containerized version which does not require a matlab license will prove very useful. Both the prior-based decomposition and dynamic analyses fill a gap in the current toolbox offerings, and I am very much looking forward to hear about these new developments.