Difference between revisions of "AnyWave:Faq"

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'''Frequently asked questions (FAQ)''' about '''AnyWave'''. If you don't have an answer to your question reading the Documentation, you may find useful information here.
 
'''Frequently asked questions (FAQ)''' about '''AnyWave'''. If you don't have an answer to your question reading the Documentation, you may find useful information here.
 +
=File formats=
 +
AnyWave can read and/or write to different file formats depending on the available plug-ins.<br/>
 +
==Read==
 +
{| class="wikitable"
 +
|-
 +
! Manufacturer !! modality !! file extension
 +
|-
 +
| AnyWave|| all modalities || *.ades
 +
|-
 +
| Micromed || EEG/SEEG || *.trc
 +
|-
 +
| EDF+ || EEG/SEEG || *.edf
 +
|-
 +
| BrainProducts || EEG/SEEG || *.vhdr
 +
|-
 +
| ANT EEProbe || EEG/SEEG || *.cnt
 +
|-
 +
| SPM|| all modalities || *.mat
 +
|-
 +
| EEGLAB|| all modalities || *.set
 +
|-
 +
| EGI || EEG/SEEG || *.mff
 +
|-
 +
| 4D neuroimaging|| MEG/EEG || No extension
 +
|-
 +
| Elekta|| MEG/EEG || *.fif
 +
|-
 +
| CTF|| MEG/EEG || *.ds
 +
|}
 +
==Export==
 +
AnyWave can export to the following formats:<br/>
 +
{| class="wikitable"
 +
|-
 +
! Manufacturer !! modality !! file extension
 +
|-
 +
| AnyWave|| all modalities || *.ades
 +
|-
 +
| EDF+ || EEG/SEEG || *.edf
 +
|-
 +
| BrainProducts || EEG/SEEG || *.vhdr
 +
|-
 +
| Elekta|| MEG/EEG || *.fif
 +
|-
 +
| MATLAB|| all modalities || *.mat (see documentation below)
 +
|}
  
−
=What are the available versions?=
+
==ADES format==
−
The current available versions are:
+
This is a simple file format used mostly to exchange data between different software. <br />
−
* Windows 64bit - Jun 2015
+
Here is a complete documentation of the [[AnyWave:ADES|ADES file format]]
−
* Mac OS X - Jun 2015
+
−
* Linux amd64 Debian 7.0 - Jun 2015. The package is also compatible with Ubuntu 14.04 and earlier versions.
+
−
 
+
−
Click on the link below to download '''AnyWave''' for your platform:<br/>
+
−
[http://meg.univ-amu.fr/AnyWave/download.html Download AnyWave]
+
−
<br/><br/>
+
−
 
+
−
Do not hesitate to report installation problems or other issues using our [https://github.com/anywave/anywave/issues BUG TRACKER]
+
−
 
+
−
=How to install AnyWave?=
+
−
==Windows==
+
−
After downloading the zip file, simply unzip it in a temporary folder and launch setup.exe
+
−
 
+
−
==Mac OS X==
+
−
The '''Mac OS X''' version of '''AnyWave''' supports '''Mac OS 10.5''' to '''10.10'''.
+
−
 
+
−
A DMG file is provided. After opening the dmg file, launch the installation of AnyWave and follow instructions.<br />
+
−
 
+
−
==Linux==
+
−
'''AnyWave''' is available as a '''Debian''' package for the '''amd64''' architecture.
+
−
 
+
−
The package should install as well on '''Ubuntu''' 64bit.
+
−
 
+
−
After downloading the .deb file, double-click on it or use the CLI interface to install the application.
+
−
 
+
−
After the package was successfully installed, you will be able to run AnyWave from a terminal by typing the command: '''anywave'''
+
−
 
+
−
=Where to get the documentation?=
+
−
The user guide is available here : http://meg.univ-amu.fr/AnyWave/AnyWave_UserGuide.pdf
+
−
 
+
−
See also the Wiki parts dedicated to developers: [[AnyWave:DeveloperCorner|Developer's corner]]
+
  
 +
==MATLAB format==
 +
A new plugin allows AnyWave to export data into a MATLAB file.<br />
 +
[[AnyWave:MATLAB|Here is a complete documentation about what you will find inside the MATLAB file when exporting data.]]
 
=Plug-ins=
 
=Plug-ins=
−
==What is a plug-in?==
+
The application is designed to be modular by using plug-ins.<br/>
−
'''AnyWave''' uses external modules called plug-ins, that are loaded at startup and extend the functionalities of the application.<br/>
+
Some plugins are provided with the application when installing:<br/>
−
Depending on the platform, plug-ins are files with different extensions.<br/>
+
- File read/export plugins.<br/>
−
On Windows systems plug-ins are '''.dll''' files where on Mac OS X systems the extension is '''.dylib'''. Linux version of AnyWave will use plugin with '''.so''' extension.<br/>
+
- Data Processing plugins like h²/r² correlations, Time/Frequency using wavelet, markers tools.<br/>
 +
AnyWave also supports MATLAB/Python plugins.<br/>
 +
==How to install a plug-in==
 +
The user may add custom plug-ins to AnyWave. Depending on the plug-in type (MATLAB, Python or Native) the location where to put the plug-in may vary.<br />
 +
We strongly recommend '''NOT''' to add plug-ins in the Application directory, as it may require administrative privileges and it also make the plug-ins available to all users on the computer.<br />
 
<br/>
 
<br/>
−
There are several types of plug-ins used by '''AnyWave''':<br/>
+
Place native plugins (*.dll *.so *.dylib) on the following folder depending of your platform:<br/>
−
- '''Reader''' plug-ins are responsible of reading data file formats.<br/>
+
- Windows: the folder is created in '''Documents\AnyWave\Plugins'''.<br/>
−
- '''Writer''' plug-ins are responsible of writing data to a data file format.<br/>
+
- Mac: the folder is created in '''/Users/johndoe/AnyWave/Plugins'''.<br/>
−
- '''Signal processing''' plug-ins will run some processing on data and present or not the results in '''AnyWave'''.<br/>
+
- Linux: the folder if created in '''/home/johndoe/AnyWave/Plugins'''.<br/>
−
- '''Display''' plug-ins are responsible of displaying specific data type. Typically, the results computed by signal processing plug-ins.<br/>
+
<br/>
 +
Place MATLAB plugins on the following folder depending of your platform:<br/>
 +
- Windows : the folder is created in '''Documents\AnyWave\Plugins\MATLAB'''.<br/>
 +
- Mac: the folder is created in '''/Users/johndoe/AnyWave/Plugins/MATLAB'''.<br/>
 +
- Linux: the folder if created in '''/home/johndoe/AnyWave/Plugins/MATLAB'''.<br/>
 +
<br/>
 +
Place Python plugins on the following folder depending of your platform:<br/>
 +
- Windows: the folder is created in '''Documents\AnyWave\Plugins\Python '''.<br/>
 +
- Mac: the folder is created in '''/Users/johndoe/AnyWave/Plugins/Python '''.<br/>
 +
- Linux: the folder if created in '''/home/johndoe/AnyWave/Plugins/Python '''.<br/>
 
<br/>
 
<br/>
  
−
==How to install a plug-in==
+
===Configure AnyWave for MATLAB compiled plugins===
−
When installing '''AnyWave''' some plug-ins are also installed, allowing to read file formats and allowing to do processing on data.<br/>
+
The last releases of MATLAB compiled plugins require the '''MATLAB 2018b''' runtime on Windows and '''MATLAB 2020a''' runtime on Mac.<br/>
−
Those plug-ins are located in a Plugin folder:
+
- Install the required MATLAB runtime for you platform (See the mathworks website to download and install the runtime)<br/>
−
* On Windows and Linux systems the folder is called ''Plugins'' and is located in the AnyWave folder.
+
- Configure AnyWave to use the correct version of the runtime (Mac and Linux only) :<br/>
−
* On Mac systems, the folder is called ''Anywave_Plugins'' and is installed in the '''/Applications''' folder.
+
The path on Mac should be something close to '''/Applications/MATLAB_Runtime/v98'''<br/>
−
 
+
The path on Linux should be something close to '''/usr/local/MATLAB/MATLAB_Runtime/v95'''<br/>
−
Adding a plug-in is done by copying the plug-in file in that folder. However, that will required administrator privileges.
+
−
 
+
−
===How to install user plug-ins===
+
−
One other way to install plug-ins is to copy them into the user's home directory.
+
−
 
+
−
Indeed, AnyWave will create a AnyWave folder in the user's home directory:
+
−
* On Windows that will be someting like: "My Documents\AnyWave" or "Documents\AnyWave".
+
−
* On Linux it can be at /home/user/AnyWave
+
−
* on Mac systems it will be located at /Users/user/AnyWave
+
−
 
+
−
This AnyWave folder will contain several other folders. The one usefull here is called Plugins.
+
−
 
+
−
Copy user plug-ins file in that directory and AnyWave will load them the next time the user launches it.
+
−
 
+
−
==MATLAB plug-in==
+
−
'''AnyWave''' offers the possibility to run signal processing plug-ins written with the '''MATLAB''' programming language.<br/>
+
−
There are two ways to run MATLAB code as plug-ins:
+
−
* You may have a MATLAB Compiled code as a standalone application.
+
−
* You may have a MATLAB scripted plug-in which is simply MATLAB code.
+
−
 
+
−
===MATLAB Compiled Plugin===
+
−
A MATLAB Compiled plugin is a standalone application that AnyWave could launch by passing it some parameters.<br />
+
−
To build that application the MATLAB Compiler is required as well as a C++ Compiler.<br />
+
−
Follow the instructions on the developer's corner page to see how to write a MATLAB plugin for AnyWave.<br />
+
−
We do not encourage providing MATLAB Compiled Code as it requires a specific version of the MCR to be installed on the computer.<br />
+
−
It is much more easier to share plug-ins written in MATLAB code.
+
−
 
+
−
===MATLAB Scripted Plugin===
+
−
If you are a mighty MATLAB programmer and thus have MATLAB installed on your computer, you may use and develop a MATLAB Scripted plugin.<br/>
+
−
A MATLAB Scripted plugin is a MATLAB function that will be called by AnyWave.<br/>
+
−
It is possible to use a MATLAB Scripted plugin written by someone else just by installing it in AnyWave.<br/>
+
−
 
+
−
====How to install a MATLAB Scripted Plugin====
+
−
AnyWave provides a specific location where to put MATLAB Scripted plug-ins:<br/>
+
−
You may use the global plugin directory or the user's plugin directory. On both locations you will find a subfolder called '''MATLAB'''.<br/>
+
−
AnyWave will look for MATLAB Scripted plug-ins in the two locations. ('''AnyWave Application directory/Plugins/Matlab''' or '''/user's home/AnyWave/Plugins/Matlab''')<br/>
+
 
<br/>
 
<br/>
−
A MATLAB Scripted plug-in is a simple folder containing files. If you want more details about MATLAB Scripted plug-ins, please refer to the [[AnyWave:WriteMatlabScripted|How to write a MATLAB Scripted plug-in]].<br/>
+
Set the path to the MATLAB runtime in the AnyWave preferences UI then restart AnyWave.
−
<br>
+
−
To summarize:<br/>
+
−
MATLAB Scripted plug-ins have to go in:'''Application dir/Plugins/Matlab'''  or '''/user's home/AnyWave/Plugins/Matlab'''
+
 
<br/>
 
<br/>
  
−
==Python plug-ins==
+
===Configure AnyWave for MATLAB scripted plugins===
−
AnyWave offers the possibility to write signal processing plug-in in Python.<br/>
+
MATLAB plug-ins can be distributed as MATLAB .m files and thus require that MATLAB is available on the computer.<br />
 +
AnyWave will call the MATLAB execution engine to run those files.<br />
 +
<br />
  
−
A Python module is provided allowing the developper to user some python methods to communicate with AnyWave.<br />
+
== Batch processing ==
−
Python 2.7 must be present on the system, and numpy 1.7 is also required as AnyWave provides data using numpy arrays.<br />
+
Some processes can be executed in batch mode, using the command line.<br/>
 +
See this section [[AnyWave::CLI|Command Line Options]] for more details.<br/>
 +
List of process that can be executed in batch mode:<br>
 +
* [[AnyWave:ICA|ICA (extracts independent components)]].
 +
* [[AnyWave:H2| H2 (computes connectivity)]].
  
−
A Python plug-in is very similar to a MATLAB Scripted Plug-in. The install procedure is the same except that you have to copy the plugin in a folder named '''Python''':<br/>
 
−
Python plug-ins have to go in:'''AnyWave application/Plugins/Python/'''  or  '''/user's home/AnyWave/Plugins/Python'''
 
  
−
=File formats=
 
−
AnyWave can read and/or write to different file formats depending on the available plug-ins.
 
  
−
For EEG data the following formats are supported for reading:
+
=Command line options=
−
* Neuroscan (.cnt)
+
AnyWave can also be launched using the command line. This will prevent any GUI to pop up on the screen.<br/>
−
* Micromed (.trc)
+
In this mode, you will be able to batch some operations, like converting files to another format or BIDSify some file.<br/>
−
* Electrode Array (.eab)
+
See this section [[AnyWave::CLI|Command Line Options]]
−
* EDF/BDF (.eeg)
+
−
* Brainvision Analyser (.vhdr)
+
−
* ADES (.ades) AnyWave simple format.
+
  
−
For MEG data the following formats are supported for reading:
+
=BIDS support=
−
* 4DNI
+
The BIDS support is under development, but there is a command line feature that can be used to launch AnyWave without any GUI and<br />
−
* CTF
+
ask it to convert a SEEG file into a BIDS compatible format and place it to a specified folder.<br />
−
* ADES (.ades) AnyWave simple format.
+
options:<br />
 +
--toBIDS indicates we want to convert a file to BIDS.<br />
 +
--bids_modality <ieeg|meg> specify what the file to convert contains (ieeg, meg).'''REQUIRED'''<br />
 +
--bids_sub <subject> BIDS subject  '''REQUIRED'''<br />
 +
--bids_task <task> BIDS task  '''REQUIRED'''<br />
 +
--bids_run <run> BIDS run index (optional)<br />
 +
--bids_acq <acq> BIDS acquisition (optional)<br />
 +
--bids_proc <proc> process (optional)<br />
 +
--bids_output <sidecars|all>  (sidecars : only generates .json and .tsv files. all: full conversion)<br />
 +
--bids_ses <session> BIDS session (optional)<br />
 +
--bids_format <edf | vhdr> (optional)<br />
 +
'''Note''':<br/>
 +
When converting MEG data, user input_folder not input_file option.<br/>
 +
Some MEG formats consists of several files in a folder, so the BIDS conversion will produce also a folder.<br/>
 +
==Example==
 +
Convert a file data.eeg containing SEEG recordings to BIDS for subject JohnDoe.<br />
 +
<syntaxhighlight lang='bash'>
 +
anywave --toBIDS --bids_modality ieeg --input_file d:\data\data.eeg --output_dir d:\data\BIDS --bids_format vhdr --bids_sub johndoe --bids_task rest
 +
</syntaxhighlight>
 +
Convert a MEG data file (4DNI) to BIDS for subject JohnDoe.<br />
 +
The run number must be specified.<br/>
 +
<syntaxhighlight lang='bash'>
 +
anywave --toBIDS --bids_modality meg --input_dir d:\data\MEG\run1 --output_dir d:\data\BIDS --bids_sub johndoe --bids_task rest --bids_run 01
 +
</syntaxhighlight>
 +
Convert a MEG data file (Elekta) to BIDS for subject JohnDoe.<br />
 +
As everything is stored in one file (.fif), no need here to specify a run number (but you can). <br/>
 +
However, the input is still a folder, so specifiy the folder in which the fif file is located.<br/>
 +
<syntaxhighlight lang='bash'>
 +
anywave --toBIDS --bids_modality meg --input_dir d:\data\MEG --output_dir d:\data\BIDS --bids_sub johndoe --bids_task rest
 +
</syntaxhighlight>
  
−
It is also possible to export to the following formats:
+
= Log files =
−
* Brainvision Analyser (.vhdr)
+
Every time an operation is launched, a log file is created by AnyWave.<br />
−
* ADES (.ades) AnyWave simple format.
+
This is also the case for command line execution.<br />
−
 
+
Depending on your platform, the log files are located in the following folder:<br/>
−
==ADES format==
+
- Windows: '''\Documents\AnyWave\Log'''<br/>
−
This is a simple file format used mostly to exchange data between different software.  
+
- Mac: '''/Users/johndoe/AnyWave/Log'''<br/>
−
This is '''NOT''' the official AnyWave format but just a media used for exchanging between software.
+
- Linux: '''/home/johndoe/AnyWave/Log'''<br/>
−
 
+
−
Here is a complete documentation of the [[AnyWave:ADES|ADES file format]]
+

Latest revision as of 10:46, 7 September 2020

Frequently asked questions (FAQ) about AnyWave. If you don't have an answer to your question reading the Documentation, you may find useful information here.

File formats

AnyWave can read and/or write to different file formats depending on the available plug-ins.

Read

Manufacturer modality file extension
AnyWave all modalities *.ades
Micromed EEG/SEEG *.trc
EDF+ EEG/SEEG *.edf
BrainProducts EEG/SEEG *.vhdr
ANT EEProbe EEG/SEEG *.cnt
SPM all modalities *.mat
EEGLAB all modalities *.set
EGI EEG/SEEG *.mff
4D neuroimaging MEG/EEG No extension
Elekta MEG/EEG *.fif
CTF MEG/EEG *.ds

Export

AnyWave can export to the following formats:

Manufacturer modality file extension
AnyWave all modalities *.ades
EDF+ EEG/SEEG *.edf
BrainProducts EEG/SEEG *.vhdr
Elekta MEG/EEG *.fif
MATLAB all modalities *.mat (see documentation below)

ADES format

This is a simple file format used mostly to exchange data between different software.
Here is a complete documentation of the ADES file format

MATLAB format

A new plugin allows AnyWave to export data into a MATLAB file.
Here is a complete documentation about what you will find inside the MATLAB file when exporting data.

Plug-ins

The application is designed to be modular by using plug-ins.
Some plugins are provided with the application when installing:
- File read/export plugins.
- Data Processing plugins like h²/r² correlations, Time/Frequency using wavelet, markers tools.
AnyWave also supports MATLAB/Python plugins.

How to install a plug-in

The user may add custom plug-ins to AnyWave. Depending on the plug-in type (MATLAB, Python or Native) the location where to put the plug-in may vary.
We strongly recommend NOT to add plug-ins in the Application directory, as it may require administrative privileges and it also make the plug-ins available to all users on the computer.

Place native plugins (*.dll *.so *.dylib) on the following folder depending of your platform:
- Windows: the folder is created in Documents\AnyWave\Plugins.
- Mac: the folder is created in /Users/johndoe/AnyWave/Plugins.
- Linux: the folder if created in /home/johndoe/AnyWave/Plugins.

Place MATLAB plugins on the following folder depending of your platform:
- Windows : the folder is created in Documents\AnyWave\Plugins\MATLAB.
- Mac: the folder is created in /Users/johndoe/AnyWave/Plugins/MATLAB.
- Linux: the folder if created in /home/johndoe/AnyWave/Plugins/MATLAB.

Place Python plugins on the following folder depending of your platform:
- Windows: the folder is created in Documents\AnyWave\Plugins\Python .
- Mac: the folder is created in /Users/johndoe/AnyWave/Plugins/Python .
- Linux: the folder if created in /home/johndoe/AnyWave/Plugins/Python .

Configure AnyWave for MATLAB compiled plugins

The last releases of MATLAB compiled plugins require the MATLAB 2018b runtime on Windows and MATLAB 2020a runtime on Mac.
- Install the required MATLAB runtime for you platform (See the mathworks website to download and install the runtime)
- Configure AnyWave to use the correct version of the runtime (Mac and Linux only) :
The path on Mac should be something close to /Applications/MATLAB_Runtime/v98
The path on Linux should be something close to /usr/local/MATLAB/MATLAB_Runtime/v95

Set the path to the MATLAB runtime in the AnyWave preferences UI then restart AnyWave.

Configure AnyWave for MATLAB scripted plugins

MATLAB plug-ins can be distributed as MATLAB .m files and thus require that MATLAB is available on the computer.
AnyWave will call the MATLAB execution engine to run those files.

Batch processing

Some processes can be executed in batch mode, using the command line.
See this section Command Line Options for more details.
List of process that can be executed in batch mode:


Command line options

AnyWave can also be launched using the command line. This will prevent any GUI to pop up on the screen.
In this mode, you will be able to batch some operations, like converting files to another format or BIDSify some file.
See this section Command Line Options

BIDS support

The BIDS support is under development, but there is a command line feature that can be used to launch AnyWave without any GUI and
ask it to convert a SEEG file into a BIDS compatible format and place it to a specified folder.
options:
--toBIDS indicates we want to convert a file to BIDS.
--bids_modality <ieeg|meg> specify what the file to convert contains (ieeg, meg).REQUIRED
--bids_sub <subject> BIDS subject REQUIRED
--bids_task <task> BIDS task REQUIRED
--bids_run <run> BIDS run index (optional)
--bids_acq <acq> BIDS acquisition (optional)
--bids_proc <proc> process (optional)
--bids_output <sidecars|all> (sidecars : only generates .json and .tsv files. all: full conversion)
--bids_ses <session> BIDS session (optional)
--bids_format <edf | vhdr> (optional)
Note:
When converting MEG data, user input_folder not input_file option.
Some MEG formats consists of several files in a folder, so the BIDS conversion will produce also a folder.

Example

Convert a file data.eeg containing SEEG recordings to BIDS for subject JohnDoe.

anywave --toBIDS --bids_modality ieeg --input_file d:\data\data.eeg --output_dir d:\data\BIDS --bids_format vhdr --bids_sub johndoe --bids_task rest

Convert a MEG data file (4DNI) to BIDS for subject JohnDoe.
The run number must be specified.

anywave --toBIDS --bids_modality meg --input_dir d:\data\MEG\run1 --output_dir d:\data\BIDS --bids_sub johndoe --bids_task rest --bids_run 01

Convert a MEG data file (Elekta) to BIDS for subject JohnDoe.
As everything is stored in one file (.fif), no need here to specify a run number (but you can).
However, the input is still a folder, so specifiy the folder in which the fif file is located.

anywave --toBIDS --bids_modality meg --input_dir d:\data\MEG --output_dir d:\data\BIDS --bids_sub johndoe --bids_task rest

Log files

Every time an operation is launched, a log file is created by AnyWave.
This is also the case for command line execution.
Depending on your platform, the log files are located in the following folder:
- Windows: \Documents\AnyWave\Log
- Mac: /Users/johndoe/AnyWave/Log
- Linux: /home/johndoe/AnyWave/Log

Retrieved from "https://meg.univ-amu.fr/index.php?title=AnyWave:Faq&oldid=26138"