Computational protocol: In vivo assessment of human brainstem cerebrovascular function: a multi-inversion time pulsed arterial spin labelling study

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Protocol publication

[…] The time series of images was motion corrected using 3dvolreg within AFNI (http://afni.nimh.nih.gov/afni). Brain extraction was performed on the first image of the raw motion corrected series and the CSF calibration image with the brain extraction tool within the FMRIB Software Library v5.0 (FSL-http://fsl.fmrib.ox.ac.uk). The CSF image was registered to the perfusion series using FLIRT within FSL and a mask of the lateral ventricles was used to calculate M0,CSF. This mask was made by first applying a threshold at 95% of the maximum signal intensity to the CSF image and then using AFNI's 3dclust to find the largest cluster of voxels in a cube covering a large area of the brain, including both ventricles, in this masked image. The equilibrium magnetization for arterial blood (M0,blood) was then calculated according to methods previously described by Wong et al with CSF as a reference. [...] Comparison of the physiologic parameters between different ROIs was performed with RM-ANOVA in SPSS Statistics for Windows, Version 20.0 (IBM Corp., Armonk, NY, USA) using ROI (i.e., BS, CB, OP, and GM) as the independent factor and CBF, aBV, AAT, and TAT as dependent factors. A two-way RM-ANOVA was performed with the data of the HC experiment in which physiologic state (i.e., NC or HC) was added as an independent factor. Follow-up pairwise comparisons were performed as appropriate using the Bonferroni correction. In some cases, the assumption of sphericity for the data did not hold (i.e., differences between ROI averages do not have equal variances). In those cases, the Greenhouse-Geiser correction for sphericity was used and this is reported by using FcorrGG instead of F in Results. Results are stated as mean±standard deviation, except where explicitly stated as mean±standard error of the mean to illustrate the confidence in the obtained mean values. […]

Pipeline specifications

Software tools AFNI, BET, FSL, SPSS
Applications Miscellaneous, Magnetic resonance imaging, Functional magnetic resonance imaging
Organisms Homo sapiens
Diseases Brain Stem Neoplasms