Difference between revisions of "MEG Software and Analysis"

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* [[External MEG Analysis Toolboxes | Other Software packages]]
 
* [[External MEG Analysis Toolboxes | Other Software packages]]
 
==== 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.
 
 
* [https://megcore.nih.gov/pyctf/parsemarks.py parsemarks.py download]
 
 
<syntaxhighlight lang="bash">
 
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.
 
</syntaxhighlight>
 
 
parsemarks2.py provides provides more control over the output.
 
 
* [https://megcore.nih.gov/pyctf/parsemarks2.py parsemarks2.py download]
 
 
<syntaxhighlight lang="bash">
 
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
 
</syntaxhighlight>
 
 
* [https://megcore.nih.gov/pyctf/parsemarks_report.py parsemarks_report.py download]
 
: Requires the ''xlsxwriter'' module for writing Excel files.
 
 
<syntaxhighlight lang="bash">
 
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
 
</syntaxhighlight>
 
  
 
==== Stimulus Presentation Software ====
 
==== Stimulus Presentation Software ====

Revision as of 13:07, 4 April 2020

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.

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!

Miscellaneous Documentation

  • Adobe-ps.png SensLayout-275 — a color picture showing the sensor names and relative locations (ps).
  • Pdf.png SensLayout-275 - a color picture showing the sensor names and relative locations (pdf).
  • Pdf.png File Formats - CTF MEG data file format