MEG Software and Analysis
MEG Core pyctf tools ported to Python 3
pyctf tools are a collection of Python scripts useful in the analysis of data sets collected from the CTF scanner. These tools have been rewritten using modern Python 3 syntax following standard coding conventions. Most of these programs will run unmodified under MacOS, Windows, and the various versions of Linux with a Python 3.4 distribution or later installed. Python programs requiring modules not included in the standard Python library are indicated.
parsemarks.py usage: parsemarks.py [-h] [-l] dataset Extract the marks from the marker file associated with dataset and print themin a useful format. positional arguments: dataset path to CTF dataset or MarkerFile.mrk (required) optional arguments: -h, --help show this help message and exit -l the marks are labeled in the output. Useful for debugging.
parsemarks2.py provides provides more control over the output.
parsemarks2.py usage: parsemarks2.py [-h] [-l] [-m marker...] [-s] dataset Extract the marks from the marker file associated with dataset and print them in a useful format. positional arguments: dataset path to CTF dataset (required) optional arguments: -h, --help show this help message and exit -l the marks are labeled in the output. Useful for debugging. -m marker the specified mark(s) is reported (default is all markers) -s shows a list of markers in dataset and exits
- Requires the xlsxwriter module for writing Excel files.
parsemarks_report.py usage: parsemarks_report.py [-h] [-v] studydir Reports on the marker set from every dataset directory under a study directory. MEG studies consists of a collection of datasets, each with its own MarkerFile.mrk, organized under a top level (studydir) directory. Output is an excel file stored in your ~/excel folder. positional arguments: studydir path to a toplevel directory holding a set of dataset directories (required) optional arguments: -h, --help show this help message and exit
Stimulus Presentation Software
PsychoPy: Psychology software in Python PsychoPy is an open-source application that allows you to run a wide range of neuroscience, psychology and psychophysics experiments. It’s a free, powerful alternative to Presentation™ or to e-Prime™, written in Python (a free alternative to Matlab™ ).
Presentation: NeuroBehavioral Systems (NBS), Inc. Presentation® is a stimulus delivery and experiment control program for neuroscience written for Microsoft Windows.
E-prime 3: Psychology Software Tools E-Prime® 3.0 software for behavioral research. Build your own experiments using E-Prime’s easy-to-use graphical interface. Design, collect, and analyze data – all within a few hours!
MEG Data Analysis
This section covers all aspects of MEG data analysis. The following pages assume that you have AFNI installed and have a reasonably good idea of how to use it.