Date: 04-24-2018
Link: http://rpubs.com/navona/OPT_ToNI_pilots

This script compares data from two pilot participants scanned on the new ToNI UT2 scanner (UT99998 and UT99999) and two participants (UT10001 and UT10004) to 4 participants from LA1, on metrics central to structural, functional, and diffusion imaging.

The scatterplots provide a visual overview of the data distribution. All values have been Z-transformed. The dotted line indicates 1.5 SDs away from mean, and the solid line indicates 2.0 SDs away from mean.

The associated tables provide definitions for all metrics, and an indication of if the UT2 participants appear to be different from the LA1 participants, defined by >= 2.0 SDs away from mean.

Structural

source: T1-w
QC pipeline: MRIQC
citation: https://mriqc.readthedocs.io/en/latest/iqms/t1w.html

metric definition count
Measures based on noise measurements
cjv Coefficient of joint variation. High values relate to heavy head motion and large INU artifacts. 0
cnr Contrast-to-noise ratio. Evaluates how separated tissue distributions of GM and WM are. Higher values indicate better quality. 0
snr_csf Signal-to-noise ratio, in CSF. Calculated within the tissue mask. 0
snr_gm Signal-to-noise ratio, in GM. Calculated within the tissue mask. 0
snr_wm Signal-to-noise ratio, in WM. Calculated within the tissue mask. 0
snr_total Signal-to-noise ratio, across CSF, GM, and WM. Calculated within the tissue mask. 0
snrd_csf Dietrich’s SNF, in CSF. Uses the air background as reference. 0
snrd_gm Dietrich’s SNF, in GM. Uses the air background as reference. 0
snrd_wm Dietrich’s SNF, in WM. Uses the air background as reference. 0
snrd_total Dietrich’s SNF, across CSF, GM, and WM. Uses the air background as reference. 0
qi_2 Mortamet’s quality index. Calculation of goodness-of-fit of a chi-square distribution on the air mask. 0
Measures based on information theory
efc Entropy-focus criterion. Indication of ghosting and blurring induced by head motion. Lower values are better. 0
fber Foreground-background energy ratio. Mean energy of image values within the head relative to outside the head. Higher values are better. 0
Measures targeting specific artifacts
inu_med Median of the INU field. Values closed to 1.0 are better. 0
inu_range Range of the INU field. Values closed to 1.0 are better. 0
qi_1 Proportion of voxels with intensity corrupted by artifacts. Lower values are better. 1
wm2max White-matter to maximum intensity ratio. Values should be around the interval [0.6, 0.8]. 0
Other measures
fwhm_avg Spatial distribution of the image intensity values in units of voxels. Lower values are better. 0
rpve_csf Residual partial volume effect, of CSF. Lower values are better. 0
rpve_gm Residual partial volume effect, of GM. Lower values are better. 0
icvs_csf Volume fractions, of CSF. Should move within a normative range. 0
icvs_gm Volume fractions, of GM. Should move within a normative range. 0
icvs_wm Volume fractions, of WM. Should move within a normative range. 0

Diffusion

source: DTI
QC pipeline: ENIGMA DTI
citation: https://github.com/josephdviviano/qcmon

metric definition count
maxRELrms Maximum relative root mean square of displacement. Measure of head motion. Should be low. 0
maxABSrms Maximum RMS displacement relative to a single reference volume. Measure of head motion. Should be low. 0
meanRELrms Average relative root mean square of displacement. Measure of head motion. Should be low. 0
meanABSrms Average RMS displacement relative to a single reference volume. Measure of head motion. Should be low. 0
outcount_bX Count of number of temporal outliers. 1
outmean_bX Mean value of temporal outliers, across all directions. 1
outmax_bX Max value of temporal outliers, across all directions. 1
driftpercent Percentage of drift of global signal, across all directions. 1
drift_bX Drift of global signal mean, across all directions. 1
gmean_bX Global signal mean, across all directions. 0
tsnr_bX Average temporal SNR, across all directions. Should be high. 1
clipcount Number of voxels with clipped amplitude (i.e. >= 4095). 0

Functional

QC pipeline: FMRIPREP
source: Resting State 1 (RS1)

source: Resting State 2 (RS2)

source: Faces task

metric definition RS1 RS2 Faces
CSF Average signal inside the CSF mask across time. 0 0 0
WhiteMatter Average signal inside the WM mask across time. 0 0 0
GlobalSignal Global-signal within the whole-brain mask. 0 0 0
stdDVARS Standardized derivative of RMS variance over voxels. 0 0 0
non.stdDVARS Non-standardized derivative of RMS variance over voxels. 0 0 0
vx.wisestdDVARS Voxel-wise-standardized derivative of RMS variance over voxels. 0 0 0
FramewiseDisplacement Quantification of the estimated bulk-head motion. 0 0 0