[ENH] Extend BIDS for Motion data (BEP029) #981
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| # Motion | ||
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| For information on how to cite this extension when referencing it in the context of the academic literature, please read [Citing BIDS](../introduction.md#citing-bids). | ||
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| Motion datasets formatted using this specification are available on the | ||
| [BIDS examples repository](https://github.com/bids-standard/bids-examples#motion-datasets) | ||
| and can be used as helpful guidance when curating new datasets. | ||
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| ## Motion recording data | ||
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| {{ MACROS___make_filename_template( | ||
| "raw", | ||
| datatypes=["motion"], | ||
| suffixes=["motion", "channels", "events"]) | ||
| }} | ||
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| A wide variety of motion capture systems are used in human research, resulting in different proprietary data formats. | ||
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| This BIDS extension deals with common outputs from motion capture systems such as positions, orientations, or their time derivatives. | ||
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| The extension is not limited to motion data in physical space but also encompasses simulated movement in virtual space, as far as these are comparable to movements in physical space. | ||
| Other dynamic objects than human body parts whose motion is tracked may as well be included as tracked objects. | ||
| This specification does not include raw camera footages (from camera-based or optical motion capture recordings), but includes the positions or orientations computed using such data. | ||
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| In this specification, positions (and their time derivatives) are represented as Cartesian coordinates along up to three spatial axes, | ||
| and orientations (and their time derivatives) are represented as Euler angles. | ||
| However, to cover recordings from computer graphics applications (for example, virtual 3D motion or immersive virtual reality recording in physical space), | ||
| orientations are also allowed to be represented as [quaternions](https://en.wikipedia.org/wiki/Quaternion). | ||
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| In this case, the quaternion channels can be distinguished from channels containing Euler angles based on the entries in columns `component` and `units` in the `*_channels.tsv` file. | ||
| See subsection on `Channels description` for further details. | ||
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| Motion data from one tracking system MUST be stored in a single `*_motion.tsv` file. | ||
| A tracking system is defined as a group of motion channels that share hardware properties (the recording device) and software properties (the recording duration and number of samples). | ||
| For example, if the position time series of multiple optical markers is processed via one recording unit, this MAY be defined as a single tracking system. | ||
| Note that it is not uncommon to have multiple tracking systems to record at the same time. | ||
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| Each tracking system MUST have its own `*_tracksys-<label>_motion.tsv` file, where `<label>` is a user-defined keyword to be used to identify each file belonging to a tracking system. | ||
| This is especially helpful when more than one tracking system is used. | ||
| Data from different tracking systems MUST be stored in different `*_tracksys-<label>_motion.tsv` files, | ||
| each of which is accompanied by `*_tracksys-<label>_motion.json` and `*_tracksys-<label>_channels.tsv` files. | ||
| Between `tracksys-<label>` entity and `*_motion.tsv`, `*_motion.json`, or `*_channels.tsv` suffixes, optional [`acq-<label>`](../appendices/entities.md#acq) or [`run-<index>`](../appendices/entities.md#run) entity MAY be inserted. | ||
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| One column in the `*_tracksys-<label>_motion.tsv` file represents one data channel. | ||
| The ordering of columns MUST match the order of rows in the `*_channels.tsv` file for unambiguous assignment. | ||
| All relevant metadata about a tracking systems is stored in accompanying sidecar `*_tracksys-<label>_motion.json` file. | ||
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| The source data from each tracking system in their original format, if different from `.tsv`, | ||
| can be stored in the [`/sourcedata` directory](../common-principles.md#source-vs-raw-vs-derived-data). | ||
| The original data format MAY hold more metadata than currently specified in the `*_motion.json` file. | ||
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| When multiple tracking systems are used to record motion or motion capture is used alongside the recording of other BIDS modalities and recordings should be interpreted together, | ||
| it is adviced to provide a possibility to synchronize recordings. | ||
| The prefered way to do so is to use the acquisition time of the first data point of recordings and | ||
| to store this information in the `acq_time` column of the [`*_scans.tsv`](../modality-agnostic-files.md#scans-file) file. | ||
| The Note that the [BIDS date time format](../common-principles.md#units) allows optional fractional seconds, which SHOULD be used to maximize the precision of the syncronization. | ||
| Only if the precision of the synchronization is not high enough, the `*_events.tsv` file SHOULD be used to syncronize recordings. | ||
| In this file, the start- and stop time of the recording of a system are specified in relation to a system to synchronize with. | ||
| If more than two systems are to be synchronized, it is up to the user to indntify the "main" system. | ||
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| In case a tracking system provides time information with every recorded sample, | ||
| these time information MAY be stored in form of latencies to recording onset (first sample) in the `*_motion.tsv` file. | ||
| If a system has uneven sampling rate behavior, the `LATENCY` channel can be used to share these information. | ||
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| To store events alongside motion data when there are multiple tracking systems simulatenously in use, it is RECOMMENDED to designate a tracking system to the events file. | ||
| Such an events file name SHOULD include the `tracksys` key and looks like `sub-<label>[_ses-<label>]_task-<label>[_acq-<label>]_tracksys-<label>[_run-<index>]_events.tsv`. | ||
| Event latencies can then be related to motion samples of multiple tracking systems also by using `acq_time` column entries in the `*_scans.tsv`. | ||
| The same principle applies when the events file is saved alongside a simultaneously recorded non-motion data (for example EEG). | ||
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| ### Sidecar JSON (`*_motion.json`) | ||
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| #### Task information | ||
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| {{ MACROS___make_sidecar_table("motion.motionTaskInformation") }} | ||
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| #### Hardware information | ||
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| {{ MACROS___make_sidecar_table("motion.motionHardware") }} | ||
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| #### Insitution information | ||
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| {{ MACROS___make_sidecar_table("motion.motionInstitutionInformation") }} | ||
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| #### Motion specific fields | ||
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| Motion specific fields MUST be present: | ||
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| {{ MACROS___make_sidecar_table("motion.motionRequired") }} | ||
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| Motion specific fields SHOULD be present: | ||
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| {{ MACROS___make_sidecar_table("motion.motionRecommended") }} | ||
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| #### Example `*_tracksys-<label>_motion.json` | ||
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| ```JSON | ||
| { | ||
| "SamplingFrequency": 60, | ||
| "SamplingFrequencyEffective": 60.00197437, | ||
| "TaskName": "BIDS Motion fictive example", | ||
| "TrackingSystemName": "IMU Right Hand", | ||
| "TaskDescription": "walking and talking", | ||
| "InstitutionAddress": "Fictive address", | ||
| "InstitutionName": "Fictive Institution", | ||
| "MotionChannelCount": 18, | ||
| "RecordingDuration": 4667.641106, | ||
| "RotationRule": "right-hand", | ||
| "RotationOrder": "ZXY", | ||
| "SpatialAxes": "FRU", | ||
| "SubjectArtefactDescription": "n/a", | ||
| "TrackedPointsCount" : 2, | ||
| "ACCELChannelCount": 6, | ||
| "GYROChannelCount": 6, | ||
| "MAGNChannelCount": 6, | ||
| "Manufacturer": "BWSensing", | ||
| "ManufacturersModelName": "BW-IMU600", | ||
| } | ||
| ``` | ||
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| In this example, the `*_motion.json` contains data from one tracking system consisting of two | ||
| [inertial measurement units (imu)](https://en.wikipedia.org/wiki/Motion_capture#Inertial_systems). | ||
| If there are additional tracking systems (for example [optical motion capture](https://en.wikipedia.org/wiki/Motion_capture#Optical_systems)), | ||
| data from these MUST be stored as separate files like `*_tracksys-omcA_motion.tsv` and `*_tracksys-omcB_motion.tsv`. | ||
| All specified tracking systems MAY share `tracked_point` defined in `*_channels.tsv`, when tracking devices are placed on the same object or body part. | ||
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| Note that the onsets of the recordings SHOULD be stored in the study key file [(`scans.tsv`)](../modality-agnostic-files.md#scans-file). | ||
| Here, date-time information MUST be expressed as indicated in [Units](../common-principles.md#units). | ||
| The [`scans.tsv`](../modality-agnostic-files.md#scans-file) file contains the filename and the acquisition time of a recording, | ||
| which MAY be used to synchronize multiple recordings. | ||
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| ## Channels description (`*_channels.tsv`) | ||
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| {{ MACROS___make_filename_template( | ||
| "raw", | ||
| datatypes=["motion"], | ||
| suffixes=["channels"]) | ||
| }} | ||
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| This file is REQUIRED as it makes it easy to browse or query over larger collections of datasets. | ||
| The REQUIRED columns are channel `name`, `component`, `type`, `tracked_point` and `units`. | ||
| Any number of additional columns MAY be added to provide additional information about the channels. | ||
| The `*_tracksys-<label>_channels.tsv` file SHOULD give additional information about individual recorded channel, | ||
| some of which my not be found summarized in `*_motion.json`. | ||
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| The columns of the channels description table stored in `*_channels.tsv` are: | ||
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| {{ MACROS___make_columns_table("motion.motionChannels") }} | ||
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| ### Restricted keyword list for channel component | ||
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| Restricted keyword list for column `component`. | ||
| When using quaternions to represent orientations, | ||
| the axial components that corresponds to the three spatial axes MUST be specified as "quat_x", "quat_y", "quat_z", and the non-axial component as "quat_w". | ||
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| | **Keyword** | **Description** | | ||
| | ----------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------- | | ||
| | x | Position along the X-axis, or rotation about the X-axis among the Euler angles that represent the orientation, or magnetic field strength along the X-axis. | | ||
| | y | Position along the Y-axis or rotation about the Y-axis among the Euler angles that represent the orientation, or magnetic field strength along the Y-axis. | | ||
| | z | Position along the Z-axis or rotation about the Z-axis among the Euler angles that represent the orientation, or magnetic field strength along the Z-axis. | | ||
| | quat_x | Quaternion component associated with the X-axis. | | ||
| | quat_y | Quaternion component associated with the Y-axis. | | ||
| | quat_z | Quaternion component associated with the Z-axis. | | ||
| | quat_w | Non-axial quaternion component. | | ||
| | n/a | Channels that have no corresponding spatial axis. | | ||
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| ### Restricted keyword list for channel type | ||
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| Restricted keyword list for column `type` in alphabetic order. | ||
| Note that upper-case is REQUIRED: | ||
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There was a problem hiding this comment. not a blocker for merging this PR, but before release, we must clarify how channel types are shared between modalities. I have opened a new issue for this: |
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| | **Keyword** | **Description** | **Modalities to be shared with** | | ||
| | ----------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------- | | ||
| | ACCEL | Accelerometer channel, one channel for each spatial axis. Column `component` for the axis MUST be added to the `*_channels.tsv` file (x, y, or z). | [fNIRS](./near-infrared-spectroscopy.md#near-infrared-spectroscopy) | | ||
| | ANGACC | Angular acceleration channel, one channel for each spatial axis. Column `component` for the axis MUST be added to the `*_channels.tsv` file (x, y, or z). | NONE | | ||
| | ANGVEL | Angular velocity channel, one channel for each spatial axis. Column `component` for the axis MUST be added to the `*_channels.tsv` file (x, y, or z). | None | | ||
| | GYRO | Gyrometer channel, one channel for each spatial axis. Column `component` for the axis MUST be added to the `*_channels.tsv` file (x, y, or z). | [fNIRS](./near-infrared-spectroscopy.md#near-infrared-spectroscopy) | | ||
| | JNTANG | Joint angle channel between two fixed axis belonging to two bodyparts. Angle SHOULD be defined between proximal and distal bodypart in `deg`. | NONE | | ||
| | LATENCY | Latency of samples in seconds from recording onset. MUST be in form of `ss[.000000]` , where [.000000] is an optional subsecond resolution between 1 and 6 decimal points. | ALL | | ||
| | MAGN | Magnetic field strength, one channel for each spatial axis. Column `component` for the axis MUST be added to the `*_channels.tsv` file (x, y or z). | [fNIRS](./near-infrared-spectroscopy.md#near-infrared-spectroscopy) | | ||
| | MISC | Miscellaneous channels. | ALL | | ||
| | ORNT | Orientation channel, one channel for each spatial axis or quaternion component. Column `component` for the axis or quaternion label MUST be added to the `*_channels.tsv` file (x, y, z, quat_x, quat_y, quat_z, or quat_w). | [fNIRS](./near-infrared-spectroscopy.md#near-infrared-spectroscopy) | | ||
| | POS | Position in space, one channel for each spatial axis. Column `component` for the axis MUST be added to the `*_channels.tsv` file (x, y or z). | NONE | | ||
| | VEL | Velocity, one channel for each spatial axis. Column `component` for the axis MUST be added to the `*_channels.tsv` file (x, y or z). | NONE | | ||
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| ### Example `*_channels.tsv` | ||
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| ```Text | ||
| name component type tracked_point units | ||
| t1_acc_x x ACCEL LeftFoot m/s^2 | ||
| t1_acc_y y ACCEL LeftFoot m/s^2 | ||
| t1_acc_z z ACCEL LeftFoot m/s^2 | ||
| t1_gyro_x x GYRO LeftFoot rad/s | ||
| t1_gyro_y y GYRO LeftFoot rad/s | ||
| t1_gyro_z z GYRO LeftFoot rad/s | ||
| … | ||
| t2_acc_x x ACCEL RightWrist m/s^2 | ||
| t2_acc_y y ACCEL RightWrist m/s^2 | ||
| t2_acc_z z ACCEL RightWrist m/s^2 | ||
| t2_gyro_x x GYRO RightWrist rad/s | ||
| t2_gyro_y y GYRO RightWrist rad/s | ||
| t2_gyro_z z GYRO RightWrist rad/s | ||
| ``` | ||
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should each page also be listed in the redirect map of the mkdocs.yml?
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It was like this, so I just added the motion. But happy to change it to what makes most sense :)
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@Remi-Gau would that make sense? After all, motion has never been introduced to the spec with something like
'04-modality-specific-files/0X-motion.md'but gets into the spec withmodality-specific-files/motion.md