1000 Functional Connectomes Project News

NKI-Rockland Sample: Release 7 Now Available

Cameron Craddock — Wed, 24 Jun 2015 2:16:18 GMT

Dear Colleagues,

We are proud to announce Release 7 of the NKI-Rockland Sample (NKI-RS). This release contains updates for the Cross-sectional NKI-RS Lifespan (PI: Michael P. Milham) and Longitudinal Developmental Connectomics (PI: Michael P. Milham). We are also proud to announce the inclusion of the Real-time Default Network Neurofeedback (PI: R. Cameron Craddock) study, which contains data from a real-time fMRI based default network neurofeedback task in addition to data from multi-source interference and moral dilemma tasks. More information about the various studies can be found at the Enhanced NKI-RS website: http://fcon_1000.projects.nitrc.org/indi/enhanced/.

Release 7 neuroimaging data along with data from variety of psychiatric, neuropsychological, and fitness assessments are available via the Collaborative Informatics Neuroimaging Suite (COINS) Data Exchange with a fully executed DUA. Please refer to ftp://www.nitrc.org/fcon_1000/htdocs/indi/NKI-RSI_HowToAccessData.pdf for more information about accessing the data from COINS.

Users who do not wish to get a DUA can download the neuroimaging data with limited phenotypic information from NITRC. Release 6 and 7 data will be available on NITRC in July, using a new distribution framework.

Best,
the NKI-RS team

--
Cameron Craddock, PhD

Director of Imaging, Center for the Developing Brain
Child Mind Institute
childmind.org
445 Park Avenue (entrance on 56th Street)
New York, NY 10022

Director, Computational Neuroimaging Laboratory
Nathan S. Kline Institute for Psychiatric Research
www.rfmh.org/nki
1040 Old Orangeburg Road
Orangeburg, NY, 10962

FCP/INDI: 181 Multiband R-fMRI/DTI Datasets Released

Michael Milham — Mon, 07 Jan 2013 1:09:29 GMT

** 1000 Functional Connectomes Project (FCP) / International Neuroimaging Data-sharing Initiative (INDI) Data Release Announcement **

RELEASE NAME: Enhanced NKI-RS ‘Lite’ Release
PROVIDER: Enhanced Nathan Kline Institute - Rockland Sample (NKI-RS)
DATA TYPE: Resting State fMRI (TR = 645, 1400, 2500), Diffusion Tensor Imaging (137 directions/2mm isotropic)

ANNOUNCEMENT: We are pleased to announce the release of imaging data and limited phenotyping (age, sex, handedness) for the first 181 participants of the Enhanced NKI-RS. The Enhanced NKI-RS is a large scale NIMH-funded imaging effort dedicated to the acquisition and open distribution of functional and structural imaging data for 1000 community-ascertained individuals between the ages of 6.0 and 85.0 years old, over a 4-year period. Comprehensive psychiatric, cognitive and behavioral phenotyping are obtained from participants to ensure maximal value in efforts to reveal brain-behavior relationships. Basic laboratory measures are collected as well.

The following scans were attempted for each participant:
- multiband resting state functional MRI (TR = 645/3mm isotropic; 10 min)
- multiband resting state functional MRI (TR = 1400/2mm isotropic; 10 min)
- standard resting state functional MRI (TR = 2500/3mm isotropic; 5 min)
- multiband diffusion tensor imaging (137 directions/2mm isotropic; <7 min).

Additionally, we attempted to obtain the following scans: 1) breath-holding and 2) visual checkerboard stimulation (blocked design).

NOTES:
1) A 24-subject test-retest pilot multiband dataset for this protocol is available: http://fcon_1000.projects.nitrc.org/indi/pro/eNKI_RS_TRT/FrontPage.html
2) A publication describing the NKI-RS effort (Nooner et al., 2012) can be found at: http://www.frontiersin.org/Brain_Imaging_Methods/10.3389/fnins.2012.00152/abstract
3) In order to protect participant privacy, access to the corresponding high dimensional phenotypic data does require a confidentiality and non-disclosure agreement (see Data-Sharing Policy section of website for details; tentative distribution date for high dimensional phenotyping data is Feb 1, 2013).

DATA COLLECTION PERIOD: March, 2012 – November, 2012
SHARING TYPE: Unrestricted, prospective/pre-publication
DISTRIBUTION FORMATS: DICOM, NIFTI
DOWNLOAD LOCATION: http://fcon_1000.projects.nitrc.org/indi/enhanced/index.html

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Michael P. Milham, MD, PhD
Director, Center for the Developing Brain
Senior Research Scientist
Child Mind Institute

Research Psychiatrist
Deputy Director of Human Imaging at the Center for Advanced Brain Imaging
Nathan S. Kline Institute for Psychiatric Research

The Neuro-Bureau Brain-Art Competition 2012

Michael Milham — Thu, 10 May 2012 5:19:50 GMT

NEURO-BUREAU BRAIN-ART COMPETITION 2012
http://www.neurobureau.org/BrainArt/

Submission Deadline: 11:59PM CDT, Friday, June 1st, 2012

Award Notification: June 11th during the OHBM Annual Meeting, Beijing.

In order to recognize the beauty and creativity of artistic renderings emerging from the neuroimaging community, we are launching the second annual Brain-Art Competition.

Countless hours are devoted to the creation of informative visualizations for communicating neuroscientific findings. The Brain-Art Competition aims to recognize this often unappreciated aspect of the publication process, and highlight the artistic creativity of our community.

We are inviting researchers to submit their favorite unpublished works for entry. Both team and single-person entries are welcomed. The competition will have four award categories:

1) Best Representation of the Human Connectome
2) Best Educational Brain Illustration
3) Best Abstract Brain Illustration
4) Best Humorous Brain Illustration
5) Best Video Illustration of the Brain

Sponsored by: Child Mind Institute (http://www.childmind.org/)

Announcing the INDI Summer of Sharing 2012

Michael Milham — Wed, 02 May 2012 7:13:24 GMT

THE INTERNATIONAL NEUROIMAGING DATA-SHARING INITIATIVE (INDI) SUMMER OF SHARING 2012
http://fcon_1000.projects.nitrc.org/

Open science initiatives are transforming the neuroimaging community. Researchers who once struggled to obtain 20-30 datasets now have unrestricted access to thousands of scans, including data obtained from developing, aging and clinical populations. Equally important, the sharing of data analysis scripts and code is becoming increasingly common, thereby enhancing the dissemination of knowledge and capabilities among laboratories – as well as facilitating replication efforts. Although exciting, we are only at the beginning. The success of open science initiatives remains dependent upon continued community participation.

Against this background, the International Neuroimaging Data-sharing Initiative (INDI) is pleased to announce the launch of its 2012 Summer of Sharing – an effort dedicated to the sustenance and acceleration of data and analytic resource sharing among imaging community members. In order to accomplish its goal the INDI Summer of Sharing initiative is requesting pledges for the contribution of:

1) DATA: Resting state fMRI and/or diffusion data employed in published studies, along with any available meta-data you’d like to share (See INDI Retro for previously shared datasets; examples include Kelly C. et al., 2011 Bio Psych, Keller C. et al., 2011 PNAS, and Power J. et al., 2012 Neuroimage).
2) ANALYTIC RESOURCES: Python, Matlab, BASH, C/C++ - we’re not choosy! INDI is actively promoting the sharing of analytic scripts and codes employed in published and/or ongoing studies through NITRC and GitHub – if you post them, we’ll help to make sure you’re recognized for it.
3) OPEN SCIENCE EVENTS: Just provide us the information and we’ll help to get the word out!
4) MISCELLANEOUS RESOURCES: Atlases, parcellation schemes, reference resources, etc. – everyone can benefit from them.

We are actively asking investigators around the world to get involved in the sharing process. Already, the following resources are scheduled for sharing this summer:
1) The Autism Brain Imaging Data Exchange (ABIDE): a global, multisite consortium of laboratories dedicated to the study of autism that will release an aggregate dataset that is expected to consist of nearly 500 individuals with autism, and their matched typically developing controls.
2) The Enhanced NKI Rockland Sample: a recently launched large-scale, R-fMRI and DTI cross-sectional, community ascertained sample of individuals between 6 and 85 years of age, accompanied by a deep phenotypic protocol that broadly samples psychiatrically relevant behavioral domains.
3) Brainhack: a Neuro-Bureau resource (http://brainhack.org/) that points to collaborative projects in the field; the resource will be complemented by the Brainhack 2012 Unconference – a workshop that will blend the “unconference” and “hackathon” concepts to create a unique collaborative experience for participants interested in advancing analytic techniques and resources for functional and structural imaging.
4) The Configurable Pipeline for the Analysis of Connectomes (C-PAC): Building on the success of the release of the 1000 Functional Connectomes Project analysis scripts, the INDI team will be releasing a plug-and-play Nipype-based pipeline package that is easily configurable to accomplish a broad array of resting-state fMRI analyses.
5) DPARSF and REST: With the new releases of MATLAB-based user-friendly pipelines of Data Processing Assistant for Resting-State fMRI (DPARSF 2.2) and Resting-State fMRI Data Analysis Toolkit (REST 1.8) (www.restfmri.net), users can acquire resting-state fMRI measures efficiently (by parallel computing) and conveniently (by GUI or command line).
6) Power et al. 2011 (Neuron): The authors are now sharing the summary community assignments from their work on fcMRI networks (http://sumsdb.wustl.edu/sums/directory.do?id=8293343&dir_name=power_Neuron11), and will release a suite of scripts through NITRC this summer, so that others can replicate these analyses and carry out related work. Additionally, later this summer, the dataset used for this work will be released through INDI.
7) The Child Mind Institute (CMI) Librarian Initiative: Comprehensive hand-vetted and sorted reference libraries for various literatures, including Resting State fMRI and Diffusion Tensor Imaging are now available via Mendeley, with monthly updates scheduled (http://www.mendeley.com/profiles/cmi-librarian/).

It is our hope that this list is just the beginning. We will follow with updates throughout the summer months. The success of open science depends on all of us – so get involved, and Share That Brain!

Contact us at INDI_SummerOfSharing@childmind.org to make a pledge or learn more about how to get involved.

The International Neuroimaging Data-sharing Initiative (INDI) is now sponsored by the Child Mind Institute (http://childmind.org).

The Quiron-Valencia Sample is now Available in INDI PRO

Maarten Mennes — Mon, 07 Nov 2011 5:44:52 GMT

Dear Users,

We are pleased to announce the release of a new prospective sample in INDI Prospective! The release can be found here: http://fcon_1000.projects.nitrc.org/indi/pro/Quiron-Valencia.html

The Quiron-Valencia sample is contributed by Luis Marti-Bonmati, Maria de la Iglesia Vaya and the Spanish Resting State Network. This sample will have a quarterly release frequency. The first release contains 45 resting state datasets from an adult community sample. Demographic data contain age and sex, but are intended to include the Achenbach questionnaires with future releases.

This sample represents the 7th sample in the INDI prospective section. Three samples have completed their acquisition, while the four other ones still adhere to their release frequency.

Next up: datasets contributed by Andy James, including data from cocaine addicts. This sample is planned for release early December.

Happy Downloading,
The INDI Team

Train-39 Dataset released in INDI retro

Maarten Mennes — Fri, 26 Aug 2011 7:30:25 GMT

Dear Users,

We are pleased to announce the release of a new dataset in INDI Retrospective. The release can be found here: http://fcon_1000.projects.nitrc.org/indi/retro/Train-39.html

The TRAIN-39 dataset is contributed by Art Kramer, Walter Boot, and Kirk Erickson and was intended to investigate how the brain acquires complex skills. The dataset contains data for 39 participants imaged while performing a variety of complex video games. All instructions and behavioral parameters/results are available on the webpage. Finally, references to the original studies using the data are provided.

Of note, the TRAIN-39 dataset is the first dataset in INDI that does not contain resting state scans. This does not mean you cannot investigate functional connectivity style measures in these data as you can e.g. choose to regress out the task parameters (e.g., Fair et al. 2007, A method for using blocked and event-related fMRI data to study "resting state" functional connectivity, Neuroimage - http://www.ncbi.nlm.nih.gov/pubmed/17239622) or look at connectivity during the task conditions (e.g., Friston et al., 1997, Psychophysiological and modulatory interactions in neuroimaging, NeuroImage - http://www.ncbi.nlm.nih.gov/pubmed/9344826).

As always, feel free to contact us with any questions, concerns etc.

Happy Training,
The INDI Team

ps. Coming soon: the first data from the Spanish resting state network in INDI pro.

ADHD-200 Global Competition Test Dataset Released

Michael Milham — Mon, 11 Jul 2011 4:41:51 GMT

ADHD-200 GLOBAL COMPETITION TEST DATASET RELEASED

We are pleased to announce the release of the ADHD-200 test dataset. Data from the following sites is included in the release:
1) Brown
2) KKI
3) NYU
4) OHSU
5) Peking
6) Pitt
** Each site’s test data can be found under its ‘Releases’ section on the ADHD-200 page ( http://fcon_1000.projects.nitrc.org/indi/adhd200/ ). A combined file, that contains the full test dataset (‘ADHD200_Combined_TestRelease.001.001.tar.gz‘) can be found under the ‘All Releases’ tab located at the bottom of the ADHD-200 web page. **

The current release includes data from 172 participants that passed quality control (visual inspection and max Euclidean displacement < 4mm; 259 datasets had been contributed in total). The data transfer and prep process for the NeuroIMAGE site is still being finalized – we anticipate releasing this data by Wed, July 6 at the latest (the site is anticipated to provide an additional 20-30 datasets).

As a reminder, the entry submission deadlines are as follows:
1. The Highest Performance Imaging-Based Diagnostic Classification Algorithm for ADHD: August 30, 2011
2. The Most Innovative Neuroscientific Examination of ADHD: August 1, 2011

Due to the recent interest expressed by a number of individuals who first learned about the competition at the OHBM meeting, we will extend the competition registration deadline to July 8, 2011

Good luck to all participants – we are excited to see your results!

ADHD-200 Data Corrections and Test-Set Update

Michael Milham — Fri, 24 Jun 2011 10:15:40 GMT

Dear all,

I am writing with two updates. I’ll start with the bad news (and apologies), then follow with the good.

On the bad news front, while preparing the protocol for the ADHD-200 test dataset release, Maarten Mennes unearthed an error in the primary data release. Specifically, he found that, despite our best efforts to ensure the accuracy of the data, the final phenotypic data contained several errors with respect to IQ measures at the KKI site. The errors originated in the initial translation of site-specific measures to the common phenotypic set. They went undetected in our final quality control procedures, which involve inspection of the data by two independent raters, due to deviations from the specified protocol. This is highly unfortunate, and we are deeply embarrassed by the incident. The end result is that for the KKI site, 38 of the datasets have incorrect IQ scores. After uncovering the error, Maarten conducted an exhaustive dataset-wide quality control check, using an automated protocol written by our new research programmer (Sharad Sikka). This automated check was followed with manual inspection of any suspicious values. The search verified the integrity of the primary ADHD-200 dataset. Across all 776 datasets, the only additional discrepancies were that: 1) the sex of 4 of the 222 NYU participants was incorrectly specified, due to a conflict between information entered at the scanner (and preserved in the DICOM) and that entered by the clinical assessor (chart review was employed to reconcile these discrepancies), 2) 4 of the 79 OHSU participants were noted to have discrepancies – specifically, the sex of one participant was incorrectly specified, while for 3 participants, age was incorrectly specified, and 3) sex was incorrectly specified for 1 of 194 Peking/Beijing participants. Updated ADHD-200 site release files and a quick-fix .csv file will be available on 6/27.

Once again, we sincerely apologize for these errors, and any inconvenience they have caused. We hope that the accuracy checking steps described above will alleviate any concerns about the presence of further errors in the data.

2) We are on target for the July 1 release of the test dataset. Data from all but one site have been received, yielding a total of 254 potential test datasets, with 175 passing both visual inspection and the requirement for a maximum of 4mm movement in Euclidean space. Our team will use the automated phenotypic data-check system described above, followed by manual verification of all data-values by two independent raters, to ensure an error-free test-set data release.

Realizing the potential inconvenience resulting from errors in the training dataset, we will extend the due date for final entries for the diagnostic classification portion of the competition to August 30, 2011.

Sincerely,
Mike

Neuro-Bureau Announces the Brain-Art Competition 2011

Daniel Margulies — Thu, 12 May 2011 3:08:12 GMT

The Brain-Art Competition
http://www.neurobureau.org/BrainArt/

Submission Deadline: 11:59PM CDT, Sunday, June 5th, 2011
Award Notification: June 28th, 9PM at the Cirque du Cerveau Gala (during the OHBM Annual Meeting), Musée National des Beaux-Arts du Québec.

In order to recognize the beauty and creativity of artistic renderings emerging from the neuroimaging community, we are launching the first annual Brain-Art Competition.

Countless hours are devoted to the creation of informative visualizations for communicating neuroscientific findings. The Brain-Art Competition aims to recognize this often unappreciated aspect of the publication process, and highlight the artistic creativity of our community.

We are inviting researchers to submit their favorite unpublished works for entry. Both team and single-person entries are welcomed. The competition will have four award categories:
1) Best 3-Dimensional Brain Rendering
2) Best Representation of the Human Connectome
3) Best Abstract Brain Illustration
4) Best Comical Brain Illustration

Additionally, we will have a Best Hand-Drawing of the Brain “door-prize” competition beginning at 8pm at the Cirque du Cerveau Gala to be held on June 28th at the 2011 OHBM Annual Meeting in Quebec City. Materials for hand-drawing will be provided at time of entry to gala. A digital gallery containing submissions will be made available prior to the gala.

Sincerely,
Daniel Margulies, Cameron Craddock & The Neuro Bureau

ADHD-200 Announces 2011 Global Competition

Michael Milham — Fri, 11 Mar 2011 2:00:21 GMT

Despite advances in understanding aspects of the etiology of some developmental neuropsychiatric disorders, translating these insights into clinical practice has remained daunting. Significant obstacles include the lack of reliable and valid biomarkers and an insufficient understanding of the underlying pathophysiology. We believe that a community-wide effort focused on advancing functional and structural imaging examinations of the developing brain will accelerate the rate at which neuroscience can inform clinical practice.

To recruit the global scientific community to address childhood psychiatric illness, we are pleased to announce the 'ADHD-200 Global Competition.' Investigators across all disciplines and at all levels of training are invited to participate in a competition to identify:

1) The Highest Performance Imaging-Based Diagnostic Classification Algorithm for ADHD. Participants will develop and train a diagnostic classifier (ADHD-Combined type, ADHD-Inattentive type, typically developing control) based on the ADHD-200 datasets (http://fcon_1000.projects.nitrc.org/indi/adhd200/index.html) that contain structural and resting-state fMRI datasets for 285 individuals diagnosed with ADHD and 491 typically developing individuals. On July 1, 2011 a test set comprised of previously unreleased datasets will be distributed via NITRC, without diagnostic labels. Participants will be asked to submit their diagnostic classifications for the unlabeled datasets by August 15th, 2011, along with a brief report outlining their analytic approach. The winning entry will be chosen based upon prediction accuracy. Note: The test set will include unreleased datasets from sites included in the ADHD-200 release, as well as additional sites whose data were not included in the release.

2) The Most Innovative Neuroscientific Examination of ADHD. Participants are invited to use the ADHD-200 datasets released on March 1st to address the pathophysiology of ADHD, and to submit a novel manuscript reporting their findings by August 1, 2011. Each entry will be independently scored by five 'blind' judges based upon innovation, potential impact, and elegance of analytic approach. A single winning entry will be selected based upon their composite score.

Eligibility: Individuals from all disciplines and training levels are invited to participate. Team-based and single-person entries are allowed. For team-based entries, a team representative should be specified for the purpose of communications and travel to Washington D.C. if selected as the winning entry. Individuals or teams interested in participating should notify Michael Milham of their intent by July 1, 2011 (MMilham@NKI.RFMH.ORG); entry submission directions will be provided at that time.

Award: ADHD-200 global competition winners will be invited to attend the National Institute on Drug Abuse (NIDA) pre-conference symposium preceding the Society for Neuroscience Annual Meeting in Washington D.C., where they will be publicly recognized for their accomplishment and given the opportunity to present their work. Travel costs for a representative from each winning entry will be covered courtesy of NIDA.

Award Notification Date: September 1, 2011

Sincerely,

Mike

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Michael P. Milham, MD, PhD

Research Psychiatrist
Nathan S. Kline Institute for Psychiatric Research

Leon Levy Assistant Professor of Child and Adolescent Psychiatry
NYU Langone Medical Center

Associate Director, Phyllis Green and Randolph Cowen Institute for Pediatric Neuroscience, NYU Child Study Center