Basic Electrophysiology in Brainstorm
Authors: Konstantinos Nasiotis
Invasive e-phys recordings aim in capturing the spiking activities of individual or small group of neurons. Since every spiking event is a very transient phenomenon (most spikes last around 1ms), the sampling rate of the recording system needs to be very high. Nowadays, acquisition systems can accommodate recordings from hundreds of channels from multiple multi-electrode arrays from different areas of the animal’s brain. A 10-minute recording that was used at the time of this tutorial from 224 channels (2 x 96 channel Utah arrays in PFC and TEO and one 32 channel depth electrode in the hippocampus) resulted to 10 min*60 sec*30,000 samples*224 channels* 2 bytes precision /1024 kb/1024 MB/1024 GB = ~7.5 GB. Since most recordings usually last much longer, there is a need for efficient data management and utilization of maximum processing power.
Users that have Matlab’s parallel processing toolbox, will greatly benefit from the utilization of its properties. Most functions of the electrophysiology toolbox have a checkbox where users can enable parallelization of the processes.
Additionally, it is highly recommended for users that need to analyze large files, to select a large number for memory utilization on any processes that allow users to adjust the memory used, since the speed of the processes (especially the spike sorting procedures that use demultiplexing of the raw signal) can be greatly improved by the extra memory used.
All the function that will be described on this toolbox, are located in the Electrophysiology processes tab.
Any toolboxes embedded represent the work of their respective authors and need to be appropriately cited. Links to the papers that the toolboxes correspond to are located on each section.
This tutorial uses a dataset collected from Dr. Christopher Pack’s lab (www.packlab.mcgill.ca), from a macaque monkey with a penetration chamber implanted in areas MT and MST. The recording probe consisted of 32 channels and 1 reference electrode. Users can download this tutorial data that will contain a converted Plexon acquisition system raw file (ytu288c-01_converted.bst), and an anatomy folder (Floyd MRI) that can all be imported to Brainstorm. The task for the animal was to maintain fixation on a target while a superflow stimulus was presented with different directions. The events from the stimulation system are saved along with pre-spike-sorted events.
Importing raw e-phys data
The importation of raw e-phys data into Brainstorm follows the same procedure as it does for any other raw recording. Users firstly assign a name for their protocol/study, followed by the name of the subject/monkey, and sequentially can review their raw file.
All these steps are briefly repeated here for the example e-Phys file for completeness.
When a new study needs to be analyzed, users have to create a new protocol: File -> New Protocol.
Give the Protocol name: Tutorial_e-Phys.
For the anatomy set it to: No, use individual anatomy.
Default Channel File: No, use one channel file per acquisition run.