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Support for BTi and/or 4D Neuroimaging MEG data
The BTi/4D dataformat is supported thanks to the contributions from Christian Wienbruch. It requires creating two ASCII files (.4d and .xyz) with...
USA
University of Alabama, Birmingham, USA Magnes 2500 WH
University of Colorado, Denver, USA Magnes 3600 WH & Magnes I
research www.neuromeg.org
clinical www.clinicalmeg.org
map
Chicago MEG...
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Place this script in /home/$STAGE/map/protocols, cmod +x.
Now from 'Utilities" menu of psel you could start MATLAB and run any function.
To convert data from msi format to MATLAB you would need...
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Matlab Projects
: MSI>>MATLAB by eugene kronberg : matlab code to covert 4d pdf to matlab structure
: Convert 4D MEG format to Fieldtrip format by Christian Wienbruch : Fieldtrip Support...
**If you need assistance please contact **
Europe
F.C. Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands: 275 ch whole-head
MSI>>MATLAB
MAS Configuration on LINUX
MultiUser Database setup on LINUX
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FieldTrip is a Matlab toolbox for MEG and EEG analysis that is being developed at the F.C. Donders Centre together with collaborating institutes. The FieldTrip software is released as open source...
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Install tftp (credit for documentation credit to David Sudjiman @ http://www.davidsudjiman.info/2006/03/27/installing-and-setting-tftpd-in-ubuntu/)
1. Install tftpd and related packages.
$ sudo...
MEGTools and MR-Focuss by john moran
toolbox to analyze 4d meg data
MSI>>MATLAB by eugene kronberg
matlab code to covert 4d pdf to matlab structure
Call MATLAB from MSI by eugene...
megplot.m by Dan Collins : Plot MEG or EEG time-freq channel maps. EEGLAB data format
Plot MEG data using delaunay triangulation
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from pylab import plot, show, contour, pcolor, figure, cm, colorbar, contourf,scatter
from scikits.delaunay import *
import...
Calculate the leadfields from MEG data in python
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# Copyright 2008 Dan Collins
#
# This is free software; you can redistribute it and/or modify
# it under the terms...
Give coregistered points (lpa rpa and nasion) and re
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# Copyright 2008 Dan Collins
# This is free software; you can redistribute it and/or modify
# it under the...
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#!/usr/bin/env python
# python
# Copyright 2008 Dan Collins
# This is free software; you can redistribute it and/or modify
# it under the terms of the GNU General...
MEG projection of signal weight matrix using leadfield column correlation
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porting code from matlab now……
matlab demo here....
Sourcespace projection code
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""" Source Space Projection
from meg import sourcespaceprojection
qn=array([.01, .2, -1])
grid=array([1, 1,...
Import MEG Data
This module imports MEG data and MEG coil array parameters and locations relative to the subject’s
head coordinate system.
Types of data imported:
4D Neuroimaging binary data from...
MEG TOOLBOXES
MEG Tools by John Moran
meg tools wiki
4D pdf converter into matlab structure
4D pdf to Matlab converter
MRI TOOLBOXES
stuff
MEG Scripts
Display Headshape coregistered with sensor...
Starting the program (MEG Tools)
Import MEG Data
How to use…………..
STARTING THE PROGRAM
• ·Start MATLAB
• ·Type, whstart2 followed by <ENTER> at the MATLAB prompt.
• ·Alternatively, Type , the_credits <ENTER> . Then the START button on the...
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from numpy import ceil, shape
from nifti import *
def read():
nim = NiftiImage('/home/danc/python/data/standardmri/ch2b.img')
return nim...
MRI View
MRI source space creation
This viewer is done is matplotlib http://matplotlib.sourceforge.net/. While a bit on the slow side, it gets the jobs done for coregistration and viewing...
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'''This is a simple mri viewer the mri is read using the img module with the read function
from mri import img
nim=img.read()'
import numpy...
MSI to MATLAB conversion does not have to be a pain, it could be fun :)
First, one would create pdf object:
>>pdf = pdf4D(<filename>);
where <filename> is full path to the pdf...
from pdf2py import data, channel, pdfread
datapdf = pdfread.guiwin()
datapdf =...
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Then there are some things you need to know:
You can configure all security and other settings online, using the Site Manager. When you invite other people to help build...
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coming soon
This method is quite accurate at detecting bad channels using a freq based channel poximity comparison. What is done is the fft of each channel is completed using a method described here. For each...
This is a quick and dirty set of commands to get your the fft power of your meg data.
datapdf = '/home/danc/data/0611/drawing3/01%01%01@01:01/2/c,rfDC'
from pdf2py import pdfread,channel,data
d...
Lowpass highpass and notch filter of data.
In this example, we lowpass channel 1 at 55hz with a 2nd order filter.
datapdf = '/home/danc/data/e,rfhp1.0Hz,COH'
from pdf2py import...
Using R FastICA library toolkit we preform Independent Component Analysis on MEG data.
First you need to install R and the python interface to R called 'rpy'
then install the FastICA toolkit
sudo...
PyMEG: a python magnetoencephalography project
by: Dan Collins ude.revnedcu|snilloc.nad#ude.revnedcu|snilloc.nad, University of Colorado Denver, MEG lab
Overview
PyMEG is a project written in...
Read MEG data
The 'pdf2py' is the directory in pymeg that has most if not all of the import modules for reading an manipulating 4D format MEG and other 4D files into python.
First load the...
2D MEG plot
Contour plot
Plot Headshape
Plot Sensors
First use the 4D to python reader as shown here pymeg-data-import
to reiterate to plot for example the 2D data as a simple line plot,...
Tap Overview
Tap Build Average
This is a beta version of a data tap using the python libraries to read incoming data 'chunks' as they are being acquired on the MAS.
The modules necessary...
Installation
PyMEG Installation :
GUI interaction
PyMEG GUI :
Command Line interaction
Script to do a whole bunch of processing
Read process and localize 4D MEG data : Script to do several...
Plotting Functions
headshape_vtk.py : Use VTK engine to render sensors and headshape in 3D
headshape.py : Use pylab engine to render sensors or and headshape in 3D
megcontour.py : Plot contour of...
Graphical User Interface to PyMEG
The Main Window
Features: A view of loaded data and processes preformed on data. Such as projection results, or time-frequency results, etc. Shows details on data...
Import Overview
Config objects
HeadShape objects
Header objects
Importers
Written entirely in python, modules to read the 4D MEG format data, header, headshape and config files.
Howto...
Installation of pymeg
First install python2.4 or 2.5 as well as numpy and scipy http://www.scipy.org/Download
Assuming linux is your os, do the following
Download pymeg.tgz and extract it...
Install
Installation of pymeg on linux
if using windows follow these instructions pymeg-installwin
First download and install the latest build http://server.neuromeg.org/pymeg/
** oops, our...
Leadfield Overview
Compute the leadfield for source space grid points.
To compute the leadfield we need the data file name, channel indexes returned by the 'channel' module, and one or more...
Projection Overview
Projection From Simulation
Projection using column correlation of matrices with leadfield.
A technique of source localization by correlation of any signal matrix and...
This GUI frontend allows each user to have its own database.
-Implements a database lock
Quick Access of 4d MSW tools
-psel
-acquire data
-etc
New optional Patient Selection Window (PYsel)
Export...
RELEASE NOTES
+ 090327
- 090327
**090327 moving to compatibility with python 2.6
-requires a shift from delaunay interpolation to natgrid algorithm from griddata in matplotlib...
Using leadfields pymeg-leadfield-computation, and directional and positional corrdinates of a source point, generate a simulated signal.
Import the 'simsource' module and specify coordinates
from...
SourceSpaceProjections Overview
Using the imported data (pymeg-data-import), leadfield for a spatial point (pymeg-leadfield-computation), and some directional vector, construct a spatial...
Wavelet Overview
Phase Locking Factor
Using the path to datafile, calculate the time-frequency power for one channel using morlet wavelets.
from meg import...
#read the signal data, trigger channels
datapdf = '/home/danc/python/data/0888nback/c,rfhp0.1Hz'
from pdf2py import data, channel,pdfread, pdf, readwrite
from numpy import *
d =...
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[[code type="Python"]]
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quick and dirty trigger detection.
datapdf = '/home/danc/data/e,rfhp1.0Hz,COH'
ch = channel.index(datapdf, 'trig')
d = data.read(datapdf)
d.getdata(0, d.pnts_in_file,...
Read the MEG 4d format datafile
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import dftk
import os
"Read 4d MEG file via gui or commandline argument"
#---Import pdf
"""pdf =...
Call MATLAB from MSI by eugene kronberg
script to start matlab from within msi menu
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In its beta stage, but fully functional for an nifti mri. Working on integrating and overlay function to interact with MRI and coregistered view of overlay.
At the moment, the viewer allows...
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The biomag wiki and forum, is a community supported code, documentation and discussion for bioimaging topics.
The goal of this wiki and forum is to have an access point for...
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