View source for 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.

* [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 ====

'''PsychoPy: Psychology software in Python'''
[http://www.psychopy.org 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™ ).
*[[Image:pdf.png]] [[Media:PsychoPyManual.pdf| Pyschopy documentation for release 1.90.2]]

'''Presentation: NeuroBehavioral Systems (NBS), Inc.'''
Presentation® is a stimulus delivery and experiment control program for neuroscience written for Microsoft Windows.
* [https://www.neurobs.com/presentation/docs/index_html Presentation online documentation]

'''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!''
* [https://pstnet.com/products/e-prime/ E-Prime 3.0 website]

===== MEG Data Analysis =====

This section covers all aspects of MEG data analysis. The following pages assume that you have [[afni.nimh.nih.gov|AFNI]] installed and have a reasonably good idea of how to use it.

* [[CTF DataEditor|Viewing raw data: the CTF Data Editor]]

* [[Dataset and Task Utilities|Preprocessing: Dataset and Task Utilities]]

* [[Time Frequency Analysis|Time Frequency Analysis Tools]]

* [[Head Localization and MRI Coregistration|Head Localization and MRI Co-Registration]]

* [[Source Localization - SAM|Source Localization - the SAM pipeline]]

* [[Fun Stuff - How to make a movie| Fun Stuff - How to make a movie ]]

* [[External MEG Analysis Toolboxes | Other Software packages]]

====Miscellaneous Documentation====

* [[Image:adobe-ps.png]] [[Media:SensLayout-275.ps|SensLayout-275]] — a color picture showing the sensor names and relative locations (ps).
* [[Image:pdf.png]] [[Media:SensLayout-275.pdf|SensLayout-275]] - a color picture showing the sensor names and relative locations (pdf).