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)
 +
|}
 +
 +
==ADES format==
 +
This is a simple file format used mostly to exchange data between different software. <br />
 +
Here is a complete documentation of the [[AnyWave:ADES|ADES file format]]
 +
 +
==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=
−
The application is provided with plug-ins which allow for example to read and write several data file formats, apply Time/Frequency representation to a signal, etc.
+
The application is designed to be modular by using plug-ins.<br/>
 +
Some plugins are provided with the application when installing:<br/>
 +
- File read/export plugins.<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==
 
==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 />
 
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 />
 
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 />
−
We suggest to install plug-in in the user home directory where AnyWave created special folders to place custom files.<br />
+
<br/>
−
On the Windows platform, the base directory for plug-ins should be: "My Documents\AnyWave\Plugins".<br />
+
Place native plugins (*.dll *.so *.dylib) on the following folder depending of your platform:<br/>
−
On the Mac OS X and Linux platforms, the base directory for plug-ins should be: "AnyWave/Plugins" in the user's home directory.<br />
+
- Windows: the folder is created in '''Documents\AnyWave\Plugins'''.<br/>
−
There are several types of plug-ins:
+
- Mac: the folder is created in '''/Users/johndoe/AnyWave/Plugins'''.<br/>
−
* An AnyWave native plug-in is a file (a C++ library) that must be copied directly in the root plugins directory.
+
- Linux: the folder if created in '''/home/johndoe/AnyWave/Plugins'''.<br/>
−
* A MATLAB plug-in is a directory containing several files and must be copied in the MATLAB sub-directory.
+
<br/>
−
* A Python plug-in is also a directory containing several files and must be copied in the Python sub-directory.
+
Place MATLAB plugins on the following folder depending of your platform:<br/>
−
===MATLAB Requirements===
+
- 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/>
 +
 
 +
===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.<br/>
 +
- Install the required MATLAB runtime for you platform (See the mathworks website to download and install the runtime)<br/>
 +
- Configure AnyWave to use the correct version of the runtime (Mac and Linux only) :<br/>
 +
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/>
 +
<br/>
 +
Set the path to the MATLAB runtime in the AnyWave preferences UI then restart AnyWave.
 +
<br/>
 +
 
 +
===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.<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 />
 
AnyWave will call the MATLAB execution engine to run those files.<br />
 
<br />
 
<br />
−
MATLAB plug-ins can also be compiled and distributed as a standalone application.<br />
 
−
This will required the MATLAB Runtime to be installed on the computer. The Runtime is freely available from the Mathworks web site.
 
−
== Check for plugin log files ==
 
−
=Check the log file=
 
−
Every time a process is launched a log file is created by AnyWave.<br />
 
−
This is also the case for scripted execution.<br />
 
−
<br />
 
−
Check for log files on the Log subfolder of AnyWave:<br />
 
−
[[File:log_folder.png]]<br />
 
  
−
=File formats=
+
== Batch processing ==
−
AnyWave can read and/or write to different file formats depending on the available plug-ins.
+
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)]].
  
−
For EEG data the following formats are supported for reading:
 
−
* Micromed (.trc)
 
−
* EDF+/BDF+ (.edf/.bdf)
 
−
* Brainvision Analyser (.vhdr)
 
−
* ANT EEProbe (.cnt)
 
−
* Neuroscan old format (.cnt)
 
−
* ADES (.ades) AnyWave simple format.
 
−
* SPM (*.mat)
 
−
* EEGLAB (*.set)
 
−
* EGI (*.mff)
 
  
−
For MEG data the following formats are supported for reading:
 
−
* 4DNI
 
−
* CTF
 
−
* Elekta (*.fif)
 
−
* ADES (.ades) AnyWave simple format.
 
−
 
−
It is also possible to export to the following formats:
 
−
* Brainvision Analyser (.vhdr)
 
−
* ADES (.ades) AnyWave simple format.
 
−
* MATLAB (.mat)
 
−
 
−
==ADES format==
 
−
This is a simple file format used mostly to exchange data between different software. <br />
 
−
Here is a complete documentation of the [[AnyWave:ADES|ADES file format]]
 
−
 
−
==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.]]
 
  
 
=Command line options=
 
=Command line options=
Line 78: Line 122:
 
--bids_ses <session> BIDS session (optional)<br />
 
--bids_ses <session> BIDS session (optional)<br />
 
--bids_format <edf | vhdr> (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==
 
==Example==
 
Convert a file data.eeg containing SEEG recordings to BIDS for subject JohnDoe.<br />
 
Convert a file data.eeg containing SEEG recordings to BIDS for subject JohnDoe.<br />
−
<syntax highlight lang='bash'>
+
<syntaxhighlight lang='bash'>
−
anywave --toBIDS --bids_modality ieeg --input_file data.eeg --output_dir d:\data\BIDS --bids_format vhdr --bids_sub johndoe --bids_task rest
+
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
−
</syntax highlight>
+
</syntaxhighlight>
−
= batch processing =
+
Convert a MEG data file (4DNI) to BIDS for subject JohnDoe.<br />
−
Some processes can be executed in batch mode, using the command line.<br/>
+
The run number must be specified.<br/>
−
See this section [[AnyWave::CLI|Command Line Options]] for more details.<br/>
+
<syntaxhighlight lang='bash'>
−
List of process that can be executed in batch mode:<br>
+
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
−
* ICA (extracts independent components).
+
</syntaxhighlight>
−
* H2 (computes connectivity)
+
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>
 +
 
 +
= Log files =
 +
Every time an operation is launched, a log file is created by AnyWave.<br />
 +
This is also the case for command line execution.<br />
 +
Depending on your platform, the log files are located in the following folder:<br/>
 +
- Windows: '''\Documents\AnyWave\Log'''<br/>
 +
- Mac: '''/Users/johndoe/AnyWave/Log'''<br/>
 +
- Linux: '''/home/johndoe/AnyWave/Log'''<br/>

Latest revision as of 09:46, 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

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