Page 65 - Bladder Dysfunction in the Context of the Bladder-Brain Connection - Ilse Groenendijk.pdf

Whole brain 7T-fMRI during pelvic floor muscle contraction in male subjects 63
factor 2.17 Whole-brain coverage, with the exception of the most inferior regions of the cerebellum and the caudal brainstem, was achieved using the following parameters: voxel size: 1.77x1.77x1.75mm3, matrix size: 104x127; FOV=184x223mm; number of slices: 70,TR/TE=2000/25ms; flip angle=70°; in-plane SENSE factor R=3. Whole-brain anatomical data was acquired using the MPRAGE sequence with the following parameters: voxel size 0.7x0.7x0.7mm3, matrix size: 352x353, FOV=246mm; number of slices: 249; TR/TE = 4.4/1.97s, SENSE factors R=1.6 (anterior-posterior) and R=1.5 (right-left); total acquisition time 8’35”. To account for the signal loss in infratentorial areas, a dielectric pad of calcium titanate (CaTiO3) was placed just below the inion at the back of the subjects’ heads.18
Data pre-processing All data was reconstructed on an offline workstation using dedi- cated reconstruction software (Recon Frame, Gyrotools, Zürich, Switzerland). Further data processing was done in SPM12 (Wellcome Trust Center for Neuroimaging, London, UK). Pre-processing steps included joint image realignment of the functional runs, co-registration of the anatomical image to the resulting mean functional image and smoothing of functional data with a Gaussian kernel (FWHM 2.5mm).
Data analysis For the extraction of the peak activation coordinates, anatomical and functional data was normalized to the standard brain template of the Montreal Neuro- logical Institute (MNI152).
First-level statistical analysis was conducted using the General Linear Model (GLM). Each functional task was modelled as a boxcar convolved with a canonical hemodynamic response function (HRF) and its temporal derivative as basic functions. Realignment pa- rameters were added as nuisance regressors to account for confounding motion effects. In single subjects, activation maps were thresholded at p<0.05 voxel-based family-wise error (FWE), if clusters were not found, thresholds were changed to p<0.001 (only in putamen and thalamus results). Second-level statistical analysis was conducted using a one-sample t-test on individuals’ task responses. Activation maps were thresholded at p<0.001 uncor- rected for multiple comparisons, if the cluster was not found, the threshold was changed to p<0.005 uncorrected. Both single subject and group level cortical activation maps were projected on inflated cortical surfaces created in Freesurfer and sampled halfway the grey matter (projfrac=0.5). In order to aid the inflation process, all images were first bias cor- rected (bias FWHM=18, sampling distance=2) and resliced to 1mm isotropic in SPM.
Functional connectivity analysis Connectivity analysis was performed by calculating the correlation between time series from different regions of interest (ROIs) in each single subject. ROIs were isolated using individuals’ contrast images. Where necessary, for example between primary motor and sensory regions, merged ROIs were manually separated in ITK-SNAP. Subsequently, voxel time series were extracted from each ROI
3