diff --git a/CHANGES.md b/CHANGES.md index 744de5e36d..3ec6f7428a 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -1,74 +1,101 @@ -1 Changelog -=============== +1 Changelog 1.1.1 - Improved the MEG landmark coordinates description. -- Replaced ManufacturersCapModelName in meg.json with CapManufacturer - and CapManufacturersModelName. + +- Replaced ManufacturersCapModelName in meg.json with CapManufacturer and +CapManufacturersModelName. + - Remove EEGSamplingFrequency and ManufacturersAmplifierModelName - from the meg.json. +from the meg.json. + - Improved the behavioural data description. 1.1.0 -- Added support for MEG data (merged BEP008) -- Added SequenceName field. -- Added support for describing events with Hierarchical Event Descriptors [[8.5 Task events](#heading=h.daip42kp5ndz)]. -- Added VolumeTiming and AcquisitionDuration fields [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)]. -- Added DwellTime field. +- Added support for MEG data (merged BEP008) +- Added SequenceName field. +- Added support for describing events with Hierarchical Event Descriptors [[4.3 Task events](src/04-modality-specific-files/03-task-events.md)]. +- Added VolumeTiming and AcquisitionDuration fields [[4.1 Task (including resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. +- Added DwellTime field. 1.0.2 -- Added support for high resolution (anatomical) T2star images [[8.3 Anatomy imaging data](#heading=h.fm6ipijipc08)]. -- Added support for multiple defacing masks [[8.3 Anatomy imaging data](#heading=h.fm6ipijipc08)]. -- Added optional key and metadata field for contrast enhanced structural scans [[8.3 Anatomy imaging data](#heading=h.fm6ipijipc08)]. -- Added DelayTime field [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)]. -- Added support for multi echo BOLD data [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)]. +- Added support for high resolution (anatomical) T2star images [[4.1 Anatomy imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)]. + +- Added support for multiple defacing masks [[4.1 Anatomy imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)]. + +- Added optional key and metadata field for contrast enhanced structural scans +[[4.1 Anatomy imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)] + +- Added DelayTime field [[4.1 Task (including resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. + +- Added support for multi echo BOLD data [[4.1 Task (including resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. 1.0.1 -- Added InstitutionName field [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)]. -- Added InstitutionAddress field [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)]. -- Added DeviceSerialNumber field [[8.4 Task (including resting state) imaging data](#heading=h.r8mrcau3kkcq)]. +- Added InstitutionName field [[4.1 Task (including resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. + +- Added InstitutionAddress field [[4.1 Task (including resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. + +- Added DeviceSerialNumber field [[4.1 Task (including resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. + - Added NumberOfVolumesDiscardedByUser and - NumberOfVolumesDiscardedByScanner field [[8.4 Task (including - resting state) imaging data](#heading=h.r8mrcau3kkcq)]. + NumberOfVolumesDiscardedByScanner field [[4.1 Task (including + resting state) imaging data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. + - Added TotalReadoutTime to functional images metadata list -  [[8.4 Task (including resting state) imaging - data](#heading=h.r8mrcau3kkcq)]. +  [[4.1 Task (including resting state) imaging + data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#task-including-resting-state-imaging-data)]. 1.0.1-rc1 -- Added T1 Rho maps [[8.3 Anatomy imaging - data](#heading=h.fm6ipijipc08)]. +- Added T1 Rho maps [[4.1 Anatomy imaging + data](src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md#anatomy-imaging-data)]. + - Added support for phenotypic information split into multiple files - [[8.11 Participant key file](#heading=h.pi5iigxxt8vy)]. + [[3.2 Participant key file](src/03-modality-agnostic-files.md#participants-file)]. + - Added recommendations for multi site datasets + - Added SoftwareVersions + - Added run-<run_index> to the phase encoding maps. Improved the description. + - Added InversionTime metadata key. + - Clarification on the source vs raw language. + - Added trial_type column to the event files. + - Added missing sub-<participant_label> in behavioural data file names + - Added ability to store stimuli files. + - Clarified the language describing allowed subject labels. + - Added quantitative proton density maps. 1.0.0 - Added ability to specify fieldmaps acquired with multiple parameter sets. + - Added ability to have multiple runs of the same fieldmap. + - Added FLASH anatomical images. 1.0.0-rc4 - Replaced links to neurolex with explicit DICOM Tags. + - Added sourcedata. + - Added data dictionaries. + - Be more explicit about contents of JSON files for structural (anatomical) scans. @@ -76,6 +103,7 @@ - Renamed PhaseEncodingDirection values from “x”, “y”, “z” to “i”, “j”, “k” to avoid confusion with FSL parameters + - Renamed SliceEncodingDirection values from “x”, “y”, “z” to “i”, “j”, “k” @@ -83,36 +111,54 @@ - Removed the requirement that TSV files cannot include more than two consecutive spaces. + - Refactor of the definitions sections (copied from the manuscript) + - Make support for uncompressed .nii files more explicit. + - Added BIDSVersion to dataset.json + - Remove the statement that SliceEncodingDirection is necessary for slice time correction + - Change dicom converter recommendation from dcmstack to dcm2nii and dicm2nii following interactions with the community (see [https://github.com/moloney/dcmstack/issues/39](https://github.com/moloney/dcmstack/issues/39) and [https://github.com/neurolabusc/dcm2niix/issues/4](https://github.com/neurolabusc/dcm2niix/issues/4)). + - Added section on behavioral experiments with no accompanying MRI acquisition + - Add \_magnitude.nii\[.gz\] image for GE type fieldmaps. + - Replaced EchoTimeDifference with EchoTime1 and EchoTime2 (SPM toolbox requires this input). + - Added support for single band reference image for DWI. + - Added DatasetDOI field in the dataset description. + - Added description of more metadata fields relevant to DWI fieldmap correction. -- PhaseEncodingDirection is now expressed in “x”, “y” etc. - instead of “PA” “RL” for DWI scans (so it’s the same as BOLD - scans) + +- PhaseEncodingDirection is now expressed in “x”, “y” etc. instead of “PA” +“RL” for DWI scans +(so it’s the same as BOLD scans) + - Added rec-<label> flag to BOLD files to - distinguish between different reconstruction algorithms (analogous - to anatomical scans). -- Added recommendation to use \_physio suffix for continuous recordings of motion parameters obtained by the scanner side reconstruction algorithms. + distinguish + between different reconstruction algorithms + (analogous to anatomical scans). + +- Added recommendation to use \_physio suffix for continuous recordings +of motion +parameters obtained by +the scanner side reconstruction algorithms. 1.0.0-rc1 -- Initial release +- Initial release diff --git a/mkdocs.yml b/mkdocs.yml index db90e20bd7..248df5c1b6 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -16,4 +16,13 @@ nav: - Physiological and other continous recordings: 04-modality-specific-files/04-physiological-and-other-continous-recordings.md - Behavioral experiments (with no MRI): 04-modality-specific-files/05-behavioural-experiments.md - Longitudinal and multi-site studies: 05-longitudinal-and-multi-site-studies.md + - Appendix: + - Contributors: 99-appendices/01-contributors.md + - Licenses: 99-appendices/02-licenses.md + - HED: 99-appendices/03-hed.md + - Entity-table: 99-appendices/04-entity-table.md + - Units: 99-appendices/05-units.md + - MEG file formats: 99-appendices/06-meg-file-formats.md + - MEG systems: 99-appendices/07-meg-systems.md + - Coordinate-systems: 99-appendices/08-coordinate-systems.md - The BIDS Starter Kit: https://github.com/bids-standard/bids-starter-kit diff --git a/src/02-common-principles.md b/src/02-common-principles.md index 87232d1bcc..cd234b72c1 100644 --- a/src/02-common-principles.md +++ b/src/02-common-principles.md @@ -298,7 +298,7 @@ SI derived units. In case there are valid reasons to deviate from SI units or SI derived units, the units MUST be specified in the sidecar JSON file. In case data is expressed in SI units or SI derived units, the units MAY be specified in the sidecar JSON file. In case prefixes are added to SI or non-SI units (e.g. -mm), the prefixed units MUST be specified in the JSON file (see Appendix V: +mm), the prefixed units MUST be specified in the JSON file (see [Appendix V](99-appendices/05-units.md): Units). In particular: - Elapsed time SHOULD be expressed in seconds. Please note that some DICOM diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md index 0c0c680617..781887d391 100644 --- a/src/03-modality-agnostic-files.md +++ b/src/03-modality-agnostic-files.md @@ -104,7 +104,8 @@ kept in phenotype/ folder and end with the `.tsv` extension. They can include arbitrary set of columns, but one of them has to be participant_id with matching `sub-`. As with all other tabular data, those additional phenotypic information files can be accompanied by a JSON file describing the -columns in detail (see Section 4.2). In addition to the column description, a +columns in detail (see [here](02-common-principles.md#tabular-files)). +In addition to the column description, a section describing the measurement tool (as a whole) can be added under the name `MeasurementToolMetadata`. This section consists of two keys: `Description` - a free text description of the tool, and `TermURL` a link to an entity in an diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md index fa3339ddcc..695b164bcd 100644 --- a/src/04-modality-specific-files/02-magnetoencephalography.md +++ b/src/04-modality-specific-files/02-magnetoencephalography.md @@ -43,8 +43,9 @@ task-based, resting-state, and noise recordings. If multiple Tasks were performed within a single Run, the task description can be set to `task-multitask`. The \_meg.json SHOULD contain details on the Tasks. Some manufacturers data storage conventions use folders which contain data files of -various nature: e.g., CTF’s .ds format, or 4D/BTi. Please refer to Appendix VI -for examples from a selection of MEG manufacturers. +various nature: e.g., CTF’s .ds format, or 4D/BTi. Please refer to +[Appendix VI](../99-appendices/06-meg-file-formats.md) for examples from a +selection of MEG manufacturers. The `proc` label is analogous to `rec` for MR and denotes a variant of a file that was a result of particular processing performed on the device. This is @@ -69,10 +70,10 @@ Whenever possible, please avoid using ad-hoc wording. | :--------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | | InstitutionName | RECOMMENDED. The name of the institution in charge of the equipment that produced the composite instances. | | InstitutionAddress | RECOMMENDED. The address of the institution in charge of the equipment that produced the composite instances. | -| Manufacturer | RECOMMENDED. Manufacturer of the MEG system (`CTF`, `Elekta/Neuromag`, `4D/BTi`, `KIT/Yokogawa`, `ITAB`, `KRISS`, `Other`). See Appendix VII with preferred names | -| ManufacturersModelName | RECOMMENDED. Manufacturer’s designation of the MEG scanner model (e.g. `CTF-275`). See Appendix VII with preferred names | +| Manufacturer | RECOMMENDED. Manufacturer of the MEG system (`CTF`, `Elekta/Neuromag`, `4D/BTi`, `KIT/Yokogawa`, `ITAB`, `KRISS`, `Other`). See [Appendix VII](../99-appendices/07-meg-systems.md) with preferred names | +| ManufacturersModelName | RECOMMENDED. Manufacturer’s designation of the MEG scanner model (e.g. `CTF-275`). See [Appendix VII](../99-appendices/07-meg-systems.md) with preferred names | | SoftwareVersions | RECOMMENDED. Manufacturer’s designation of the acquisition software. | -| ManufacturersModelName | RECOMMENDED. Manufacturer’s designation of the MEG scanner model (e.g. `CTF-275`). See Appendix VII with preferred names | +| ManufacturersModelName | RECOMMENDED. Manufacturer’s designation of the MEG scanner model (e.g. `CTF-275`). See [Appendix VII](../99-appendices/07-meg-systems.md) with preferred names | | SoftwareVersions | RECOMMENDED. Manufacturer’s designation of the acquisition software. | | TaskDescription | RECOMMENDED. Description of the task. | | Instructions | RECOMMENDED. Text of the instructions given to participants before the scan. This is not only important for behavioural or cognitive tasks but also in resting state paradigms (e.g. to distinguish between eyes open and eyes closed). | @@ -127,7 +128,8 @@ Specific EEG fields (if recorded with MEG) SHOULD be present: By construct, EEG when recorded simultaneously with the same MEG system , should have the same `SamplingFrequency` as MEG. Note that if EEG is recorded with a separate amplifier, it should be stored separately under a new /eeg data type -(see BEP006). +(see +[BEP006](https://docs.google.com/document/d/1ArMZ9Y_quTKXC-jNXZksnedK2VHHoKP3HCeO5HPcgLE/edit#heading=h.4k1noo90gelw)). Example: @@ -163,8 +165,9 @@ Example: ``` Note that the date and time information SHOULD be stored in the Study key file -(`scans.tsv`), see section 8.8. Scans.tsv. As it is indicated there, date time -information MUST be expressed in the following format `YYYY-MM-DDThh:mm:ss` +(`scans.tsv`), see [Scans.tsv](../03-modality-agnostic-files.md#scans-file). As +it is indicated there, date time information MUST be expressed in the following +format `YYYY-MM-DDThh:mm:ss` ([ISO8601](https://en.wikipedia.org/wiki/ISO_8601) date-time format). For example: 2009-06-15T13:45:30. It does not need to be fully detailed, depending on local REB/IRB ethics board policy. @@ -189,11 +192,11 @@ The columns of the Channels description table stored in `*_channels.tsv` are: MUST be present: -| Field name | Definition | -| :--------- | :--------------------------------------------------------------------------------------------------------------------- | -| name | REQUIRED. Channel name (e.g., MRT012, MEG023) | -| type | REQUIRED. Type of channel; MUST use the channel types listed below. | -| units | REQUIRED. Physical unit of the data values recorded by this channel in SI (see Appendix V: Units for allowed symbols). | +| Field name | Definition | +| :--------- | :----------------------------------------------------------------------------------------------------------------------------------------------------- | +| name | REQUIRED. Channel name (e.g., MRT012, MEG023) | +| type | REQUIRED. Type of channel; MUST use the channel types listed below. | +| units | REQUIRED. Physical unit of the data values recorded by this channel in SI (see [Appendix V](../99-appendices/05-units.md): Units for allowed symbols). | SHOULD be present: @@ -219,7 +222,7 @@ MLC11 MEGGRADAXIAL T sensor 1st-order grad 1200 0 n/a 50 SSS bad Restricted keyword list for field `type` | Keyword | Definition | -|------------------|------------------------------------------------------| +| ---------------- | ---------------------------------------------------- | | MEGMAG | MEG magnetometer | | MEGGRADAXIAL | MEG axial gradiometer | | MEGGRADPLANAR | MEG planargradiometer | @@ -252,7 +255,7 @@ Restricted keyword list for field `type` Example of free text for field `description` - stimulus, response, vertical EOG, horizontal EOG, skin conductance, sats, - intracranial, eyetracker + intracranial, eyetracker Example: @@ -280,32 +283,32 @@ EEG, head localization coils, and anatomical landmarks. MEG and EEG sensors: -| Field name | Description | -| :----------------------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| MEGCoordinateSystem | REQUIRED. Defines the coordinate system for the MEG sensors. See Appendix VIII: preferred names of Coordinate systems. If `Other`, provide definition of the coordinate system in `[MEGCoordinateSystemDescription]`. | -| MEGCoordinateUnits | REQUIRED. Units of the coordinates of `MEGCoordinateSystem`. MUST be `m`, `cm`, or `mm`. | -| MEGCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the MEG coordinate system system in detail. | -| EEGCoordinateSystem | OPTIONAL. Describes how the coordinates of the EEG sensors are to be interpreted. | -| EEGCoordinateUnits | OPTIONAL. Units of the coordinates of `EEGCoordinateSystem`. MUST be `m`, `cm`, or `mm`. | -| EEGCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the EEG coordinate system system in detail. | +| Field name | Description | +| :----------------------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| MEGCoordinateSystem | REQUIRED. Defines the coordinate system for the MEG sensors. See [Appendix VIII](../99-appendices/08-coordinate-systems.md): preferred names of Coordinate systems. If `Other`, provide definition of the coordinate system in `[MEGCoordinateSystemDescription]`. | +| MEGCoordinateUnits | REQUIRED. Units of the coordinates of `MEGCoordinateSystem`. MUST be `m`, `cm`, or `mm`. | +| MEGCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the MEG coordinate system system in detail. | +| EEGCoordinateSystem | OPTIONAL. Describes how the coordinates of the EEG sensors are to be interpreted. | +| EEGCoordinateUnits | OPTIONAL. Units of the coordinates of `EEGCoordinateSystem`. MUST be `m`, `cm`, or `mm`. | +| EEGCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the EEG coordinate system system in detail. | Head localization coils: | Field name | Description | | :---------------------------------- | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | HeadCoilCoordinates | OPTIONAL. Key:value pairs describing head localization coil labels and their coordinates, interpreted following the `HeadCoilCoordinateSystem`, e.g., {`NAS`: `[12.7,21.3,13.9]`, `LPA`: `[5.2,11.3,9.6]`, `RPA`: `[20.2,11.3,9.1]`}. Note that coils are not always placed at locations that have a known anatomical name (e.g. for Elekta, Yokogawa systems); in that case generic labels can be used (e.g. {`coil1`: `[12.2,21.3,12.3]`, `coil2`: `[6.7,12.3,8.6]`, `coil3`: `[21.9,11.0,8.1]`} ). | -| HeadCoilCoordinateSystem | OPTIONAL. Defines the coordinate system for the coils. See Appendix VIII: preferred names of Coordinate systems. If "Other", provide definition of the coordinate system in `HeadCoilCoordinateSystemDescription`. | +| HeadCoilCoordinateSystem | OPTIONAL. Defines the coordinate system for the coils. See [Appendix VIII](../99-appendices/08-coordinate-systems.md): preferred names of Coordinate systems. If "Other", provide definition of the coordinate system in `HeadCoilCoordinateSystemDescription`. | | HeadCoilCoordinateUnits | OPTIONAL. Units of the coordinates of `HeadCoilCoordinateSystem`. MUST be `m`, `cm`, or `mm`. | | HeadCoilCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the Head Coil coordinate system system in detail. | Digitized head points: -| Field name | Description | -| :--------------------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| DigitizedHeadPoints | OPTIONAL. Relative path to the file containing the locations of digitized head points collected during the session (e.g., `sub-01_headshape.pos`). RECOMMENDED for all MEG systems, especially for CTF and 4D/BTi. For Elekta/Neuromag the head points will be stored in the fif file. | -| DigitizedHeadPointsCoordinateSystem | OPTIONAL. Defines the coordinate system for the digitized head points. See Appendix VIII: preferred names of Coordinate systems. If `Other`, provide definition of the coordinate system in `DigitizedHeadPointsCoordinateSystemDescription`. | -| DigitizedHeadPointsCoordinateUnits | OPTIONAL. Units of the coordinates of `DigitizedHeadPointsCoordinateSystem`. MUST be `m`, `cm`, or `mm`. | -| DigitizedHeadPointsCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the Digitized head Points coordinate system system in detail. | +| Field name | Description | +| :--------------------------------------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| DigitizedHeadPoints | OPTIONAL. Relative path to the file containing the locations of digitized head points collected during the session (e.g., `sub-01_headshape.pos`). RECOMMENDED for all MEG systems, especially for CTF and 4D/BTi. For Elekta/Neuromag the head points will be stored in the fif file. | +| DigitizedHeadPointsCoordinateSystem | OPTIONAL. Defines the coordinate system for the digitized head points. See [Appendix VIII](../99-appendices/08-coordinate-systems.md): preferred names of Coordinate systems. If `Other`, provide definition of the coordinate system in `DigitizedHeadPointsCoordinateSystemDescription`. | +| DigitizedHeadPointsCoordinateUnits | OPTIONAL. Units of the coordinates of `DigitizedHeadPointsCoordinateSystem`. MUST be `m`, `cm`, or `mm`. | +| DigitizedHeadPointsCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the Digitized head Points coordinate system system in detail. | Anatomical MRI: @@ -315,18 +318,19 @@ Anatomical MRI: Anatomical landmarks: -| Field name | Description | -| :-------------------------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| AnatomicalLandmarkCoordinates | OPTIONAL. Key:value pairs of the labels and 3-D digitized locations of anatomical landmarks, interpreted following the `AnatomicalLandmarkCoordinateSystem`, e.g., {"NAS": `[12.7,21.3,13.9]`, "LPA": `[5.2,11.3,9.6]`, "RPA": `[20.2,11.3,9.1]`}. | -| AnatomicalLandmarkCoordinateSystem | OPTIONAL. Defines the coordinate system for the anatomical landmarks. See Appendix VIII: preferred names of Coordinate systems. If `Other`, provide definition of the coordinate system in `AnatomicalLandmarkCoordinateSystemDescription`. | -| AnatomicalLandmarkCoordinateUnits | OPTIONAL. Units of the coordinates of `AnatomicalLandmarkCoordinateSystem`. MUST be `m`, `cm`, or `mm`. | -| AnatomicalLandmarkCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the Head Coil coordinate system system in detail. | +| Field name | Description | +| :-------------------------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| AnatomicalLandmarkCoordinates | OPTIONAL. Key:value pairs of the labels and 3-D digitized locations of anatomical landmarks, interpreted following the `AnatomicalLandmarkCoordinateSystem`, e.g., {"NAS": `[12.7,21.3,13.9]`, "LPA": `[5.2,11.3,9.6]`, "RPA": `[20.2,11.3,9.1]`}. | +| AnatomicalLandmarkCoordinateSystem | OPTIONAL. Defines the coordinate system for the anatomical landmarks. See [Appendix VIII](../99-appendices/08-coordinate-systems.md): preferred names of Coordinate systems. If `Other`, provide definition of the coordinate system in `AnatomicalLandmarkCoordinateSystemDescription`. | +| AnatomicalLandmarkCoordinateUnits | OPTIONAL. Units of the coordinates of `AnatomicalLandmarkCoordinateSystem`. MUST be `m`, `cm`, or `mm`. | +| AnatomicalLandmarkCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the Head Coil coordinate system system in detail. | It is also RECOMMENDED that the MRI voxel coordinates of the actual anatomical landmarks for co-registration of MEG with structural MRI are stored in the `AnatomicalLandmarkCoordinates` field in the JSON sidecar of the corresponding -T1w MRI anatomical data of the subject seen in the MEG session (see section -8.3) - for example: `sub-01/ses-mri/anat/sub-01_ses-mri_acq-mprage_T1w.json` +T1w MRI anatomical data of the subject seen in the MEG session (see +[here](01-magnetic-resonance-imaging-data.md#anatomy-imaging-data) ) - for +example: `sub-01/ses-mri/anat/sub-01_ses-mri_acq-mprage_T1w.json` In principle, these locations are those of absolute anatomical markers. However, the marking of NAS, LPA and RPA is more ambiguous than that of e.g., AC and PC. @@ -352,7 +356,8 @@ or: ### Landmark photos (`*_photo.jpg`) -Photos of the anatomical landmarks and/or head localization coils (`*_photo.jpg`) +Photos of the anatomical landmarks and/or head localization coils +(`*_photo.jpg`) Template: @@ -392,7 +397,8 @@ The 3-D locations of head points and/or EEG electrode locations can be digitize and stored in separate files. The `*_acq-