NITRC Task Independent Fluctuations Discussion Forum: open-discussion

RE: Test Data

David Kennedy — Tue, 01 Sep 2009 21:32:52 GMT

It may be of interest to this 'test data' discussion that the NYU_CSC_TestRetest Project (http://www.nitrc.org/projects/nyu_trt/) has just posted a news item regarding the release of a Test-Retest Resting-State fMRI Dataset (n = 25). See http://www.nitrc.org/forum/forum.php?forum_id=1141 for further information.

When to use global signal correction

Daniel Handwerker — Fri, 17 Oct 2008 16:01:11 GMT

Since this is supposed to be a discussion list, I figured I'd try to start a discussion. I'm going to be a bit more dogmatic and provocative here than we were in the article since I figure the best way to start an active discussion here is to stake a position that I think others might want to disagree with. Please feel free to invite others who might have an interest in this topic to join the discussion.

We have a Neuroimage article in press:
The Impact of Global Signal Regression on Resting State Correlations: Are Anti-Correlated Networks Introduced?
Available online 11 October 2008
Kevin Murphy, Rasmus M. Birn, Daniel A. Handwerker, Tyler B. Jones, Peter A. Bandettini
http://www.sciencedirect.com/science/journal/10538119
If you want a copy of the article and don't have access, you can email me or one of the other authors.

In the article, we show with both theory and data how global signal regression will create anti-correlations in resting connectivity maps even when no such anti-correlations exist. We do not say that all anti-correlations following global signal regression are spurious.

1. Still, given, that we now know artificial anti-correlations will be created, is it ever appropriate regress out the global signal before running a seed-based correlation analysis?

2. If an anti-correlated network appears after global signal regression, but not after other methods that try to remove physiological noise, can we trust that the anti-correlated network has neural underpinnings? If not, is there strong evidence beyond fMRI connectivity studies using global signal regression that the default mode network has correlated and anti-correlated regions with a neural origin? The last few paragraphs of the discussion in the manuscript outline the connectivity results using some other analysis methods. I'll again note that I'm intentionally being a bit provocative here.

3. What methods should we use to remove non-neural noise in connectivity studies. In the article we use RETROICOR and Respiration*Volume/Time (RVT) correction, but there are other methods that just regress out CSF or white matter signals. What do the people in this discussion group consider their standard method?

Dan

RE: Brainscape

David Kennedy — Wed, 20 Aug 2008 12:17:59 GMT

Brainscape is now NITRC-Listed at http://www.nitrc.org/projects/brainscape/

RE: Test Data

Daniel Marcus — Thu, 22 May 2008 21:47:32 GMT

The two data sets currently on Brainscape that would be most appropriate are from Fox et.al. 2007 Neuron and Fox et.al. 2005 PNAS. Both include control subjects, around a dozen each.

These data have all been run through the standard seed-region based correlation analysis engine on Brainscape. We'd be very enthusiastic to see others run these data sets through other tools.

We're also enthusiastic to incorporate additional analysis tools into Brainscape, if anyone is interested in seeing their tools distributed as server side pipelines.

-Dan

RE: Test Data

Daniel Kimberg — Thu, 22 May 2008 20:47:32 GMT

It would be useful to know which if any of the datasets housed by the fmridc include resting data. Maybe if the readers of this forum divide it up, it wouldn't be too painful to go through all the studies. Fair et al. (2007, the ref is in the wiki for this group) also point out that you can do pretty well using the resting blocks from blocked BOLD studies.

RE: Test Data

Daniel Handwerker — Thu, 22 May 2008 20:34:44 GMT

In the previous forum thread, Daniel Marcus mentioned http://brainscape.org
It is a repository of resting state runs from multiple published studies.

Test Data

David Kennedy — Thu, 22 May 2008 20:26:50 GMT

Are there sources of test data (real or simulation) that are useful for comparing and contrasting different approaches to resting state (or rather, task independent) analysis procedures?

If so, what data?

If not, would it be a good idea, or even possible to have some such data available for common use?

Brainscape

Daniel Marcus — Tue, 13 May 2008 21:45:47 GMT

Hi all,

I thought I'd put in a plug for Brainscape (www.brainscape.org). It's a website put together by the Neuroinformatics Research Group and Neuroimaging Laboratories at Washington Univeristy. It's focused on resting state fMRI data and analysis. It includes a database of public and private data sets and and an online seed-region based correlation analysis engine. You can upload your own data and run it through preprocessing and analysis. You can optionally share your data with select colleagues or to everyone. The site currently includes a couple of public access data sets (Fox et.al. 2007 Neuron; Fox et.al. 2005 PNAS) and more are being uploaded as we speak.

The site is in beta now, so we'd love to get your comments. And your data. Feel free to submit data, in public or private mode.

The NITRC page for brainscape (a bit sparse right now) is here: http://www.nitrc.org/projects/brainscape/

Regards,
Dan Marcus
dmarcus@wustl.edu

RE: meeting at ISMRM 2008

David Kennedy — Mon, 28 Apr 2008 16:46:46 GMT

I'll be there; and also have a NITRC electronic poster (Tuesday, 5/6 at 1:30). Perhaps during or after the e-poster would be a chance to meet.

Dave Kennedy

meeting at ISMRM 2008

Daniel Handwerker — Fri, 25 Apr 2008 14:58:20 GMT

If anyone interested in the development of this resource and will be at ISMRM, perhaps we can have a group meeting and talk in person. I will be there from Saturday through Thursday morning.

Dan