MEG Software and Analysis: Difference between revisions

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==== MEG Core pyctf tools ported to Python 3====
==== MEG Data Analysis ====
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.


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.
* [https://megcore.nih.gov/pyctf/parsemarks.py parsemarks.py download]


* [[CTF Tools|The CTF Tools in a Singularity Container]]
<syntaxhighlight lang="bash">
parsemarks.py
usage: parsemarks.py [-h] [-l] dataset


* [[Pyctf|Accessing CTF Datasets from Python]]
Extract the marks from the marker file associated with dataset
and print themin a useful format.


* [[Time Frequency Analysis|Time Frequency Analysis Tools]]
positional arguments:
dataset path to CTF dataset or MarkerFile.mrk (required)


* [[Head Localization and MRI Coregistration|Head Localization and MRI Co-Registration]]
optional arguments:
-h, --help show this help message and exit
-l the marks are labeled in the ouput. Useful for debugging.
</syntaxhighlight>


* [[Source Localization - SAM|Source Localization - the SAM pipeline]]
* [https://megcore.nih.gov/pyctf/parsemarks_report.py parsemarks_report.py download]
Requires the ''xlsxwriter'' module for writing Excel files.


* [[Fun Stuff - How to make a movie| Fun Stuff - How to make a movie ]]
<syntaxhighlight lang="bash">
parsemarks_report.py
usage: parsemarks_report.py [-h] [-v] studydir


* [[External MEG Analysis Toolboxes | Other Software packages]]
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 ====
Line 53: Line 30:
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!''
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]
* [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====
====Miscellaneous Documentation====
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* [[Image:adobe-ps.png]] [[Media:SensLayout-275.ps|SensLayout-275]] — a color picture showing the sensor names and relative locations (ps).
* [[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).
* [[Image:pdf.png]] [[Media:SensLayout-275.pdf|SensLayout-275]] - a color picture showing the sensor names and relative locations (pdf).
* [[Image:pdf.png]] [[Media:FileFormats.pdf|File Formats]] - CTF MEG data file format

Revision as of 16:10, 23 September 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