Computational protocol: Mapping Long Term Functional Changes in Cerebral Blood Flow by Arterial Spin Labeling

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Protocol publication

[…] The multiple-PLD data acquired to map ATT were realigned and motion corrected as described previously. Using ASLtbx, control and label images were pair-wise subtracted and a voxel-wise parametric fit of a one-compartment kinetic model was performed using the FSL FABBER estimation routine[]. The model included spatial priors and 200 iterations. The ATT images were co-registered to their respective T1-weighted image volume using a rigid-body transformation, smoothed with a 6 mm FWHM Gaussian filter and normalized to the MNI template in SPM. [...] Reproducibility was characterized using the within-subject coefficient of variation (wsCV)[]: wsCV(%)=SD∆CBFMeanCBF∙100(2) where SDΔCBF represents the standard deviation between repeated measurements and MeanCBF is the average CBF across sessions. Reliability was measured using a two way mixed model intraclass correlation coefficient (ICC)[]: ICC=σbs2σbs2+σse2+σer2(3) where σbs2 is the between-subject variance, σse2 is the systemic error (variance between the repeated measures), and σer2 is the error variance (ICC range: 0 to 1, values > 0.75 are classified as excellent reliability)[].In order to calculate voxel-wise wsCV and ICC of resting CBF, estimates of within- and between-session variances were calculated for each voxel from a repeated measures ANOVA performed using MATLAB. A similar procedure was also applied to the ATT images to calculate the between-session and between-subject reproducibility.In addition to the voxel-wise analysis, reliability and reproducibility was also assessed within ROIs based on tissue type (grey and white matter), major lobes (frontal, parietal, temporal, occipital lobe) and selected cortical and subcortical regions (anterior cingulate cortex, amygdala, hippocampus, insular cortex, posterior cingulate cortex, somatosensory cortex and thalamus). These ROIs were defined using the Automated Anatomical Labeling (AAL) atlas[] within the WFU Pickatlas[] toolbox in SPM8. Grey and white matter masks were generated by thresholding the corresponding SPM8 probability maps by 80% and 60%, respectively. In contrast to conventional ROI analysis where reliability and reproducibility is calculated using region averaged CBF values[, ], ROI estimates were generated by multiplying the corresponding ICC and wsCV images by dichotomous masks and averaging the values within the region. To assess the effect of day-to-day variability in global CBF, all noise analyses were performed on absolute CBF (aCBF) images and on CBF images normalized by the mean grey matter value (relative CBF or rCBF). […]

Pipeline specifications

Software tools ASLtbx, AAL, SPM
Applications Magnetic resonance imaging, Diffusion magnetic resonance imaging analysis
Organisms Homo sapiens