CANDI Neuroimaging Access Point Releases

SchizBull_2008 Test Data

dnkennedy@stage.nitrcce.org (David Kennedy) — Thu, 27 Jun 2024 5:58:00 GMT

BabyBrain SampleData

dnkennedy@stage.nitrcce.org (David Kennedy) — Wed, 21 Jun 2023 12:44:00 GMT

<p>Sample Data (Input and reference Output) for initial BabyBrain Processing.</p>

Hierarchical EEG Coherence Analysis Version 1.0

dnkennedy@stage.nitrcce.org (David Kennedy) — Wed, 03 Feb 2021 12:40:00 GMT

Matlab files that accompany "Biomarkers Based on Comprehensive Hierarchical EEG Coherence Analysis: Example Application to Social Competence in Autism (Preliminary Results)" by Mo Modarres, David Cochran, David N. Kennedy, Richard Schmidt, Paula Fitzpatrick, and Jean A. Frazier.

[b]Usage Notes: BCMs.m[/b]
% BCMs.m is a Matlab Script that computes a General Brain Coherence Marker
% (BCM). BCM is based on EEG magnitude squared coherence estimate, computed
% over user specified:
% (1) Brain Regions
% (2) Time Periods
% (3) Frequency Bands
%
% by Mo H Modarres, PhD
% Eunice Kennedy Shriver Center
% University of Massachusetts Medical School
% 02/02/2021
%
% Usage:
% Step 1: Place EEG time series in a matrix X, where each column of X
% correspond to EEG data from a single EEG channel
%
% Step 2: Select the time period of analysis ;
%
% Step 3: Compute a matrix of coherence functions between all desired EEG
% pairs, using function BCMpairs.m. This step will produece
% a matrix of coherence functions with L columns,
% where L=Factorial[(No. of Columns of X) -1]
%
% Example if X consists of 4 EEG channels (4 columns of
% data), then a coherence matrix with Factorial(4-1)=3+2+1=6
% columns is produced, where each column corresponds to a coherence
% function beween unqiue pairs of EEG channels .
%
% Step 4: Perform Averaging of coherences of Step 3 over a specified
% frequency band:
%
% Step 5: Compute the averaged coherences of Step 4 over a specified brain
% region
%
% Define the following variables
%
% Tp = [k1 k2];where k1 and k2 correspond to the start and the end of
% analysis segment in Seconds
TP=[ ]
%
% Fs = Sampling frequency specified in Hertz.
Fs=

% Frq_Res= Frequency Resolution in Hertz.
Frq_Res=
% Overlap= a Value that selects the amount of overlap between two
% consecutive segments of analysis, in fraction of Fs, values
% 0.1 to 1.0; Default overlap=1;
Overlap=
% Frq_band=[f1,f2 ] where f1 and f2 correspond to the start and end of
% frequency band (in Hertz) over which the coherences will be
% averaged
Frq_band=[ ]
% ROI: Brain Region of Interest; ROI is a vector of numerical values that correpond
% to the column number of allcoh, which is a matrix of all coherence functions
% Each column is the coherence function from a single EEG pair
ROI=[]
% Output: Coh_F_Region_Average, a coherence value averaged over ROI and
% Frequency band of Interest

[b]Usage Notes: BCMpairs.m[/b]
% Computes COherence functions between any two EEG channels. Utlizes
% Matlab's MSCOHERE function, which calculates Magnitude Squared
% Coherence estimates using Welch's averaged, modified periodogram method,
% with values between 0 and 1 indicating the level of synchrocity between
% two EEG waveforms.
%
% Input Variables:
% X, Y: EEG channel data,
% Fs = Sampling frequency specified in hertz.
% Frq_Res= Frequency Resolution in hertz.
% Overlap= a Value that selects the amount of overlap between two consecutive
% segments of analysis, in fraction of Fs, values 0.1 to 1.0;
% Default overlap=1;

ReexecutabilitySurvey UnderlyingData

dnkennedy@stage.nitrcce.org (David Kennedy) — Thu, 30 Jul 2020 23:02:00 GMT

- S2_Raw_pubmed_Query_result.csv (complete PubMed query result from 1/23/2019)
- S3_CompleteSurveyData.xlsx (complete survey results)

Accompanies manuscript "An assessment of the autism neuroimaging literature for the prospects of re-executability" by Steven M. Hodge, Christian Haselgrove, Leah Honor, David N. Kennedy, Jean A. Frazier.

ReexecutabilitySurvey ExendedData

dnkennedy@stage.nitrcce.org (David Kennedy) — Thu, 30 Jul 2020 15:11:00 GMT

The complete (serialized) text of the CANDIShare re-executability survey. Accompanies manuscript "An assessment of the autism neuroimaging literature for the prospects of re-executability" by Steven M. Hodge, Christian Haselgrove, Leah Honor, David N. Kennedy, Jean A. Frazier.

Individual_Subjects_Test Subject_1

dnkennedy@stage.nitrcce.org (David Kennedy) — Mon, 18 Feb 2019 14:48:00 GMT

Individual_Subjects_Test ABCDish

dnkennedy@stage.nitrcce.org (David Kennedy) — Wed, 17 Jan 2018 22:48:00 GMT

Individual_Subjects_Test Elgan3_Phantom_UMass

dnkennedy@stage.nitrcce.org (David Kennedy) — Thu, 11 Jan 2018 18:16:00 GMT

Individual_Subjects_Test HC_001_V0.5

dnkennedy@stage.nitrcce.org (David Kennedy) — Thu, 26 Jun 2014 13:44:00 GMT

SchizBull_2008 Raw_Outlines_V1.0

dnkennedy@stage.nitrcce.org (David Kennedy) — Fri, 02 Nov 2012 18:03:00 GMT

Initial release of the .otl (outline files) version of the segmentation data for this release. While the .nii version of the segmentation were originally released, those files are derived from the cardviews-based .otl files which provide the 'outlines' of each neuroanatomic structure. While the format of these files is a bit obscure, they do represent the true 'raw' segmentation data that was in this article.