Difference between revisions of "AnyWave:CLi toBIDS"
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| − | + | =Convert files to BIDS= | |
| + | AnyWave is used by some third party softwares to process eeg/ieeg/meg files and convert them to BIDS format.<br/> | ||
| + | Here is the complete list of options to use to do so:<br/> | ||
| + | '''--toBIDS''' indicates we want to convert a file to BIDS.<br /> | ||
| + | '''--bids_modality <ieeg|eeg|meg>''' defines the data modality.'''REQUIRED'''<br /> | ||
| + | '''--bids_sub <subject>''' sets the BIDS subject '''REQUIRED'''<br /> | ||
| + | '''--bids_task <task>''' sets the BIDS task '''REQUIRED'''<br /> | ||
| + | '''--bids_ses <session>''' sets the BIDS session (optional)<br /> | ||
| + | '''--bids_run <run>''' sets the BIDS run index (optional)<br /> | ||
| + | '''--bids_acq <acq>''' sets the BIDS acquisition (optional)<br /> | ||
| + | '''--bids_proc <proc>''' sets the processing applied to the file. (optional)<br /> | ||
| + | '''--bids_output <sidecars|all>''' defines what output files will be generated (sidecars : only generates .json and .tsv files. all: full conversion)<br /> | ||
| + | '''--bids_format <edf | vhdr>''' this implies the bids_modaliy was set to eeg or ieeg. Specifies the output file format. Default is vhdr. (optional)<br /> | ||
| + | ==Examples== | ||
| + | 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_sub johndoe --bids_task rest | ||
| + | </syntaxhighlight> | ||
| + | Convert a MEG data file (4DNI) to BIDS for subject JohnDoe.<br /> | ||
| + | The run number must be specified. Note also that the input is the folder containing the MEG run, not a single file.<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> | ||
Latest revision as of 13:48, 14 April 2020
Convert files to BIDS
AnyWave is used by some third party softwares to process eeg/ieeg/meg files and convert them to BIDS format.
Here is the complete list of options to use to do so:
--toBIDS indicates we want to convert a file to BIDS.
--bids_modality <ieeg|eeg|meg> defines the data modality.REQUIRED
--bids_sub <subject> sets the BIDS subject REQUIRED
--bids_task <task> sets the BIDS task REQUIRED
--bids_ses <session> sets the BIDS session (optional)
--bids_run <run> sets the BIDS run index (optional)
--bids_acq <acq> sets the BIDS acquisition (optional)
--bids_proc <proc> sets the processing applied to the file. (optional)
--bids_output <sidecars|all> defines what output files will be generated (sidecars : only generates .json and .tsv files. all: full conversion)
--bids_format <edf | vhdr> this implies the bids_modaliy was set to eeg or ieeg. Specifies the output file format. Default is vhdr. (optional)
Examples
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_sub johndoe --bids_task restConvert a MEG data file (4DNI) to BIDS for subject JohnDoe.
The run number must be specified. Note also that the input is the folder containing the MEG run, not a single file.
anywave --toBIDS --bids_modality meg --input_dir d:\data\MEG\run1 --output_dir d:\data\BIDS --bids_sub johndoe --bids_task rest --bids_run 01Convert 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