Computational protocol: Age‐related differences in brain network activation and co‐activation during multiple object tracking

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Protocol publication

[…] Functional MRI data were processed on single‐subject level using the FMRI Expert Analysis Tool (FEAT) from the FMRIB Software Library (FSL; Smith et al., ), including spatial smoothing (FWHM = 6 mm), high‐pass filtering (sigma = 64 s), motion correction (MCFLIRT), and single‐session ICA using MELODIC (Beckmann & Smith, ).We calculated in‐scanner subject motion defined as the average root mean square of the displacement from one frame to its previous frame for each dataset, and used FMRIB's ICA‐based Xnoiseifier (FIX; Salimi‐Khorshidi et al., ) to identify and remove noise components (standard training set, threshold: 20), yielding a cleaned dataset for each subject. We used 24 motion parameters, including 6 raw realignment parameters and 24 extended parameters estimated from the realignment procedure. We did not regress out the global signal (GSR), nor the white matter or CSF. Instead, we used an ICA‐based approach to selectively regress out noise components (FIX) from each dataset, in line with recent studies evaluating benefits of different noise reduction strategies (Pruim, Mennes, Buitelaar, & Beckmann, ). The older group showed significantly more in‐scanner motion, t(43) = −3.9, p < .0001, and FIX removed a significantly higher number of components from the older group, t(19) = −2.2, p < .05, and also removed more of the variance from the raw fMRI data, both in terms of absolute and relative variance, both t(19) = −2.8, p < .05), which were significantly correlated with amount of subject motion across groups (r = .52, p < .0001).We used FreeSurfer (Fischl et al., ) for automated brain segmentation of the T1‐weighted data to obtain brain masks used for co‐registration to a standard coordinate system using FLIRT (Jenkinson & Smith, ), optimized using boundary‐based registration (BBR; Greve & Fischl, ) and FNIRT (Andersson, Jenkinson, & Smith, ,). […]

Pipeline specifications

Software tools FSL, FreeSurfer
Databases GSR
Application Functional magnetic resonance imaging