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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

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