example_ephys_bids_conversion/code/config_pybids.json

{
    "name": "bids",
    "entities": [
        {
            "name": "subject",
            "pattern": "[/\\\\]+sub-([a-zA-Z0-9]+)",
            "directory": "{subject}"
        },
        {
            "name": "session",
            "pattern": "[_/\\\\]+ses-([a-zA-Z0-9]+)",
            "mandatory": false,
            "directory": "{subject}{session}"
        },
        {
            "name": "sample",
            "pattern": "[_/\\\\]+sample-([a-zA-Z0-9]+)"
        },
        {
            "name": "task",
            "pattern": "[_/\\\\]+task-([a-zA-Z0-9]+)"
        },
        {
            "name": "acquisition",
            "pattern": "[_/\\\\]+acq-([a-zA-Z0-9]+)"
        },
        {
            "name": "ceagent",
            "pattern": "[_/\\\\]+ce-([a-zA-Z0-9]+)"
        },
        {
            "name": "tracer",
            "pattern": "[_/\\\\]+tracer-([a-zA-Z0-9]+)"
        },
        {
            "name": "stain",
            "pattern": "[_/\\\\]+stain-([a-zA-Z0-9]+)"
        },

        {
            "name": "reconstruction",
            "pattern": "[_/\\\\]+rec-([a-zA-Z0-9]+)"
        },
        {
            "name": "direction",
            "pattern": "[_/\\\\]+dir-([a-zA-Z0-9]+)"
        },
        {
            "name": "run",
            "pattern": "[_/\\\\]+run-0*(\\d+)",
            "dtype": "int"
        },
        {
            "name": "proc",
            "pattern": "[_/\\\\]+proc-([a-zA-Z0-9]+)"
        },
        {
            "name": "modality",
            "pattern": "[_/\\\\]+mod-([a-zA-Z0-9]+)"
        },
        {
            "name": "echo",
            "pattern": "[_/\\\\]+echo-([0-9]+)"
        },
        {
            "name": "flip",
            "pattern": "[_/\\\\]+flip-([0-9]+)"
        },
        {
            "name": "inv",
            "pattern": "[_/\\\\]+inv-([0-9]+)"
        },
        {
            "name": "mt",
            "pattern": "[_/\\\\]+mt-(on|off)"
        },
        {
            "name": "part",
            "pattern": "[_/\\\\]+part-(imag|mag|phase|real)"
        },
        {
            "name": "fmap",
            "pattern": "(phasediff|magnitude[1-2]|phase[1-2]|fieldmap|epi)\\.nii"
        },
        {
            "name": "recording",
            "pattern": "[_/\\\\]+recording-([a-zA-Z0-9]+)"
        },
        {
            "name": "space",
            "pattern": "[_/\\\\]+space-([a-zA-Z0-9]+)"
        },
        {
            "name": "chunk",
            "pattern": "[_/\\\\]+chunk-([0-9]+)"
        },
        {
            "name": "suffix",
            "pattern": "[._]*([a-zA-Z0-9]*?)\\.[^/\\\\]+$"
        },
        {
            "name": "scans",
            "pattern": "(.*\\_scans.tsv)$"
        },
        {
            "name": "datatype",
            "pattern": "[/\\\\]+(anat|beh|dwi|eeg|fmap|func|ieeg|meg|perf|micr|ephys)[/\\\\]+"
        },
        {
            "name": "extension",
            "pattern": "[._]*[a-zA-Z0-9]*?(\\.[^/\\\\]+)$"
        }
    ],
    "default_path_patterns": [
        "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_part-{part}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
        "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_mod-{modality}]_{suffix<defacemask>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_part-{part}]_{suffix<bold|cbv|sbref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
        "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<phase>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
        "sub-{subject}[/ses-{session}]/{datatype<dwi>|dwi}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_part-{part}]_{suffix<dwi>}{extension<.bval|.bvec|.json|.nii.gz|.nii>|.nii.gz}",
        "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}]_{fmap<phasediff|magnitude[12]|phase[12]|fieldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
        "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}]_dir-{direction}[_run-{run}]_{fmap<epi>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
        "sub-{subject}[/ses-{session}]/[{datatype<func|meg|beh>|func}/]sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<events>}{extension<.tsv|.json>|.tsv}",
        "sub-{subject}[/ses-{session}]/[{datatype<func|beh>|func}/]sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<physio|stim>}{extension<.tsv.gz|.json>|.tsv.gz}",
        "sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_run-{run}][_proc-{proc}]_{suffix<meg>}{extension}",
        "sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_run-{run}][_proc-{proc}]_{suffix<channels>}{extension<.tsv|.json>|.tsv}",
        "sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}]_{suffix<coordsystem>}{extension<.json>|.json}",
        "sub-{subject}[/ses-{session}]/{datatype<meg>|meg}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}]_{suffix<photo>}{extension<.jpg>|.jpg}",
        "[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_]{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}{extension<.json>|.json}",
        "[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_][mod-{modality}_]{suffix<defacemask>}{extension<.json>|.json}",
        "task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<bold|cbv|phase|sbref>}{extension<.json>|.json}",
        "[acq-{acquisition}_]{suffix<dwi>}{extension<.json>|.json}",
        "[acq-{acquisition}_][dir-{direction}_][run-{run}_]{fmap<phasediff|magnitude[1-2]|phase[1-2]|fieldmap>}{extension<.json>|.json}",
        "[acq-{acquisition}_][ce-{ceagent}_]dir-{direction}[_run-{run}]_{fmap<epi>}{extension<.json>|.json}",
        "task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<events>}{extension<.json>|.json}",
        "task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<physio|stim>}{extension<.json>}"
    ]
}