Sumra Bari^{1}, Pratik Kashyap^{1}, Kausar Abbas^{1}, Brenna C. McDonald^{2}, and Thomas M. Talavage^{1}

This study investigated the multi-site reliability of resting state fMRI (rs-fMRI) using Default Mode Network (DMN) connectivity and graph theory measures like mean shortest path distance, clustering coefficient, modularity, transitivity and global mean strength. Test-retest and between-site reliability for all metrics were calculated by variance component analysis using restricted maximum likelihood (REML) estimates. Test-retest reliability was found to be poor to fair and between-site reliability was consistently poor for all metrics.

**1)
Participants**:
24
healthy volunteers (13 male and 11 female; ages:22-41) participated in a total
of four imaging sessions (0-21 days apart) at two sites. (Site 1) Two imaging
sessions were conducted using a 3T General Electric Signa HDx and a 16-channel
brain array (Nova Medical). (Site 2) Two imaging sessions were conducted using
a 3T GE Discovery MR750 and a 32-channel brain array (Nova Medical). Both
imaging sessions at any given site were conducted on the same day. An
additional 15 healthy volunteers (6 male and 9 female; ages:15-29) participated
in one imaging session at Site 1.

**2) MR Data Acquisition**:
Each
imaging session (independent of site) consisted of a high-resolution (1mm
isotropic) T1-weighted scan for registration purposes and two rs-fMRI scans with
common imaging parameters across sites (TR/TE=2000/26ms; flip=35deg; 34 slices;
FOV=20cm; 3.125x3.125x3.80mm voxel size, 290 volumes).

**3) Data
Processing**:
rs-fMRI
data were processed following the pipeline from a recent study^{1} using
AFNI^{2} and FSL^{3,4}. Complete datasets of four rs-fMRI scans
were thus obtained for 17 participants after motion censoring. Using the atlas^{5},
the surviving brain volumes were divided into 278 contiguous regions-of-interest
(ROIs).

**4) Data Analysis**:
The functional connectivity
(FC) matrix for each rs-fMRI scan was computed by cross-correlating the mean
time series of each of the 278 ROIs. Resultant FC matrices were treated as
weighted undirected graphs to calculate network measures at different threshold
values of correlation. Self-connections, anti-correlations and all values less
than the threshold were set to zero and the largest component of the undirected
graph of ROIs was used for computing network measures.

DMN connectivity was calculated using a spherical seed region (18mm radius) placed at the posterior cingulate/precuneus (PCC; MNI coordinates 0,50,28). The mean time series of the seed region was correlated with each voxel time series to obtain a whole-brain correlation map. Using the independent dataset from 15 individuals (with same imaging parameters) the average whole-brain correlation map was used as a connectivity mask for the DMN to avoid circularity issues, and to obtain high quality ROIs. For averaging purposes, clusters of at least 500 voxels were observed for a correlation threshold of |r| > 0.13, resulting in four ROIs, largely located in PCC, medial frontal cortex (MFC), right and left temporal cortex (RTC and LTC respectively). The average Pearson correlation coefficient was obtained within each of these ROIs for each rs-fMRI scan and participant.

For all gray matter voxels, the temporal signal to noise ratio (tSNR) was also computed.

The reliability of each metric was calculated by
variance component analysis according to the model^{6} in equation (A)
of Figure 1, using restricted maximum likelihood (REML) estimates. All factors
are treated as random effects, with subjects and sites fully crossed, and sessions
nested within site and subject combinations. The residual term accounts for the
variance due to runs within each session, day-to-day variation at each site,
and other unexplained factors. Test-retest and between-site reliability was
estimated by equations (B) and (C) of Figure 1.

- Abbas, Kausar, et al. "Alteration of default mode network in high school football athletes due to repetitive subconcussive mild traumatic brain injury: a resting-state functional magnetic resonance imaging study." Brain connectivity 5.2 (2015): 91-101.
- Cox, Robert W. "AFNI: software for analysis and visualization of functional magnetic resonance neuroimages." Computers and Biomedical research 29.3 (1996): 162-173.
- Jenkinson, Mark, et al. "Fsl." Neuroimage 62.2 (2012): 782-790.
- Smith, Stephen M. "Fast robust automated brain extraction." Human brain mapping 17.3 (2002): 143-155.
- Shen, Xilin, et al. "Groupwise whole-brain parcellation from resting-state fMRI data for network node identification." Neuroimage 82 (2013): 403-415.
- Friedman, Lee, et al. "Test–retest and betweenâsite reliability in a multicenter fMRI study." Human brain mapping 29.8 (2008): 958-972.
- Cicchetti, Domenic V. "Guidelines, criteria, and rules of thumb for evaluating normed and standardized assessment instruments in psychology." Psychological assessment 6.4 (1994): 284.

Figure 1. Equations used for
reliability analysis.

Table 1.
Reliability
values for
DMN.

Table 2.
Test-Retest
Reliability values for network measures at each correlation threshold.

Table 3.
Between-Site Reliability
values for network measures at each correlation threshold.

Figure 2.
Percentage
variance due to each component in the model, at different correlation threshold
values, for DMN and network measures: shortest path distance (SPD); clustering
coefficient (CC); modularity (Q); transitivity (T); global mean strength (GMS).