Bruno Colombet- Platforms
- Common options that may be used
- pick_channels
- Default behavior for montages and markers
- Example
AnyWave can be run from the command line to do several operations like converting files to BIDS format or run processing on data.
The command line interface accepts options with values.
The option to run plugin is --run
The option to specify the data file to process is --input_file
Platforms
Windows:
Be sure the anywave application path is added to the system PATH.
You can also specify the full path to the application in your bash commands.
Linux:
If you installed either using the debian package or by building yourself from source codes, the installer automatically creates a link to the application in /usr/bin/anywave. So the anywave command is always found.
MacOS:
When installing the AnyWave package, a symbolic link is added into your system, so the anywave command is available when using the Terminal.
Common options that may be used
| option | value | description |
|---|---|---|
| --input_file | file path | set the input file to load |
| --run | plugin name or json file | run the specified plugin on data |
| --input_dir | directory path | set the input directory |
| --output_dir | directory path | set the output directory |
| --output_file | file name | set the output file name |
| --output_prefix | name | set the output prefix of the output file |
| --output_suffix | name | set the output suffix of the output file |
| --hp | value in Hz | high pass filter to apply |
| --lp | value in Hz | low pass filter to apply |
| --notch | value in Hz | notch filter to apply |
| --marker_file | file path | absolute path to .mrk file to use |
| --montage_file | file path | absolute path to .mtg file to apply |
| --create_montage | [bipolar_ieeg none] | bipolar_ieeg: create a bipolar SEEG montage on the fly. none: ignore all montage files |
| --pick_channels | channels list | allows to quickly use a montage using the channels specified. |
| --use_markers | markers labels | filter input data by using only data marked by the specified markers labels |
| --skip_markers | markers labels | filter input data by avoiding data marked by the specified markers labels |
| --output_format | [ades edf vhdr matlab fiff] | this defines a format to use when exporting to a data file |
| --log_dir | directory path | absolute path to a directory where to send log files. The path must exist. |
| --skip_bad_chanels | true,false,yes,no default is true | Set it false to force anywave to also add bad channels to processing input. |
pick_channels
this option allows to bypass --montage_file option by specifying a list of channels to use from the input file specified.
Example:
anywave --run h2 --input_file <file> --pick_channels "A1,A2,A3" .... Run h2 on input file using only channels A1, A2 and A3. (This will ignore any other options like --montage_file and --create_montage.
anywave --run <process> --input_file <file> --pick_channels "A1-A2, A3-A4, B2-B3"Run process on input file using a short bipolar montage (A1-A1 A3-A4 B2-B3)
Default behavior for montages and markers
When specifying a data file to load, AnyWave will check for the presence of a montage file (.mtg) and a marker file (.mrk) associated with the data.
If those files are found they will be used.
The montage and marker default files, have the same path name than the data file with the extra extension of .mtg/.mrk
If no montage file is found, then no montage will be applied and the default as recorded montage will be used.
If no marker file is found, then no markers will be loaded, but some data file already contains markers depending of the format provided by the manufacturer, thus these markers will be used.
If you want to specify another montage or marker file, you must use the --montage_file and --marker_file options.
Example
Run ica computation on MEG data file.
anywave --run ica --modality MEG --hp 1 --lp 80 --input_file d:\data\meg\1\cr,fDC --output_dir d:\data\results