Group Analysis in FieldTrip of Time-Frequency Responses: A Pipeline for Reproducibility at Every Step of Processing, Going From Individual Sensor Space Representations to an Across-Group Source Space Representation

Abstract

An important aim of an analysis pipeline for magnetoencephalographic (MEG) data is that it allows for the researcher spending maximal effort on making the statistical comparisons that will answer his or her questions. The example question being answered here is whether the so-called beta rebound differs between novel and repeated stimulations. Two analyses are presented: going from individual sensor space representations to, respectively, an across-group sensor space representation and an across-group source space representation. The data analyzed are neural responses to tactile stimulations of the right index finger in a group of 20 healthy participants acquired from an Elekta Neuromag System. The processing steps covered for the first analysis are MaxFiltering the raw data, defining, preprocessing and epoching the data, cleaning the data, finding and removing independent components related to eye blinks, eye movements and heart beats, calculating participants' individual evoked responses by averaging over epoched data and subsequently removing the average response from single epochs, calculating a time-frequency representation and baselining it with non-stimulation trials and finally calculating a grand average, an across-group sensor space representation. The second analysis starts from the grand average sensor space representation and after identification of the beta rebound the neural origin is imaged using beamformer source reconstruction. This analysis covers reading in co-registered magnetic resonance images, segmenting the data, creating a volume conductor, creating a forward model, cutting out MEG data of interest in the time and frequency domains, getting Fourier transforms and estimating source activity with a beamformer model where power is expressed relative to MEG data measured during periods of non-stimulation. Finally, morphing the source estimates onto a common template and performing group-level statistics on the data are covered. Functions for saving relevant figures in an automated and structured manner are also included. The protocol presented here can be applied to any research protocol where the emphasis is on source reconstruction of induced responses where the underlying sources are not coherent.

Alpha oscillations do not implement gain control in early visual cortex but rather gating in parieto‐occipital regions

“…2.9 | Source space data analysis AMI was computed in source space using dynamical imaging of coherent sources (DICS; Gross et al, 2001) spatial filter approach as implemented in Fieldtrip (Andersen, 2018;Oostenveld et al, 2011).…”

Reducing the efforts to create reproducible analysis code with FieldTrip

“…The analysis pipeline in (24) is well-documented and itself a good demonstration of a reproducible analysis pipeline in the FieldTrip ecosystem. Nevertheless, it consists of a complex set of 10 analysis scripts and 46 functions, which, without the extensive documentation that has been provided by the author, would be challenging to reuse and reproduce the results.…”

Software and resources for experiments and data analysis of MEG and EEG data

“…This means that an average can be made across these warped source models, since each source in each warped brain would be aligned with a corresponding source in the template brain. This strategy is followed in Andersen (2018b). Examples of both will be shown below.…”