Table 5. Spatial and temporal indices of MRI data quality selected from the Preprocessed Connectome Project.

Spatial Metrics	Description
They have been computed for all structural MRI (sMRI), Diffusion Tensor Imaging (DTI), and Resting State functional MRI (R-fMRI) datasets unless indicated otherwise. All are released for each dataset in ABIDE II (file and link of release pending). See Figs 3 and 4 and Supplementary Fig. 1 for illustrations of the distribution of a selection of spatial and temporal metrics within and across collection.
Contrast-to-noise ratio (CNR) 50 (sMRI only)	MGM intensity—MWM intensity/SDair intensity. Larger values reflect a better WM GM distinction.
Signal-to-noise ratio (SNR) 50	MGM intensity/SDair intensity. Larger values reflect less noise
Artifactual voxel detection (Qi1) 51 (sMRI only)	* voxels with intensity corrupted by artifacts/ *voxels in the background. Larger values reflect more artifacts which likley due to motion or image instability.
Entropy Focus Criteria (EFC) 65, †	Shannon’s entropy of each voxel's intensity used to measure ghosting and blurring due to head motion. Larger values reflect more blurring likley to motion or techincal differences.
Smoothness of Voxels 62 (FWHM) †	Full-width half maximum of the spatial distribution of the image intensity values. Larger values reflect more spatial smoothing maybe due to motion or technical differences.
Foreground to Background Energy Ratio (FBER) †	M energy of image intensity (i.e., mean of squares) within the head relative to that of outside the head. Larger values reflect higher signal in relation to noise.
Ghost to Signal Ratio (GSR) 66, †	M signal in the ‘ghost’ image divided by the M signal within the brain. Larger values reflect more ghosting likley due to physiological noise, motion, or technical issues.
Temporal Metrics (R-fMRI* and DTI only)
Mean framewise displacement- Jenkinson (mFD) 52, ‡	Sum absolute displacement changes in the x, y and z directions and rotational changes around them. Rotational changes are given distance values based on changes across the surface of a 50 mm radius sphere. Larger values reflect more movement.
% and * volumes with FD>0.2 mm ‡	% and *volume to volume motion >0.2 mm FD. Larger values reflect more movement.
Standardized DVARS 63, ‡	Spatial SD of the data temporal derivative normalized by the temporal SD and autocorrelation. Larger values reflect larger frame-to-frame differences in signal intensity due to head motion or scanner instability.
Outlier Detection 67, †	M fraction of outliers in each volume per 3dToutcount AFNI command. Higher values reflect more outlying voxels, which may be due to scanner instability or RF artifacts.
Global Correlation (GCORR) 64, ‡	M correlation of all combinations of voxels in a time series. Illustrates differences between data due to motion/physiological noise. Larger values reflect a greater degree of spatial correlation between slices, which may be due to head motion or ‘signal leakage’ in simultaneous multi-slice acquisitions.
Median Distance Index 67, ‡	M distance (1—spearman’s rho) between each time-point's volume and the median volume using AFNI’s 3dTqual command. Higher values reflect greater differences between subsequent frames, which may be due to head motion or technical issues.

*For all R-fMRI data temporal metrics have been computed after discarding the first 5 time points of the time series which were field map corrected if field maps were provided (only in the SDSU_1 data collection). Computation of all spatial metrics excluded absolute zero background values.

^† For R-fMRI data these metrics are computed on mean functional data.

^‡ For R-fMRI these metrics are computed on time series data. M, Mean; GM, Gray Matter; WM, White Matter; s.d., Standard Deviation.