diff --git a/src/04-modality-specific-files/02-magnetoencephalography.md b/src/04-modality-specific-files/02-magnetoencephalography.md index 2929cf9c20..6e9ed18fa3 100644 --- a/src/04-modality-specific-files/02-magnetoencephalography.md +++ b/src/04-modality-specific-files/02-magnetoencephalography.md @@ -81,38 +81,38 @@ Whenever possible, please avoid using ad-hoc wording. Specific MEG fields MUST be present: -| Field name | Definition | -| :------------------ | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400) | -| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the MEG instrument (i.e. 50 or 60) | -| DewarPosition | REQUIRED. Position of the dewar during the MEG scan: `upright`, `supine` or `degrees` of angle from vertical: for example on CTF systems, upright=15°, supine = 90°. | -| SoftwareFilters | REQUIRED. List of temporal and/or spatial software filters applied, or ideally key:value pairs of pre-applied software filters and their parameter values: e.g., {"SSS": {"frame": "head", "badlimit": 7}}, {"SpatialCompensation": {"GradientOrder": Order of the gradient compensation}}. Write `n/a` if no software filters applied. | -| DigitizedLandmarks | REQUIRED. Boolean ("true" or "false") value indicating whether anatomical landmark points (i.e. fiducials) are contained within this recording. | -| DigitizedHeadPoints | REQUIRED. Boolean (`true` or `false`) value indicating whether head points outlining the scalp/face surface are contained within this recording. | +| Field name | Definition | +| :------------------ | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400) | +| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the MEG instrument (i.e. 50 or 60) | +| DewarPosition | REQUIRED. Position of the dewar during the MEG scan: `upright`, `supine` or `degrees` of angle from vertical: for example on CTF systems, upright=15°, supine = 90°. | +| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"SSS": {"frame": "head", "badlimit": 7}, "SpatialCompensation": {"GradientOrder": "Order of the gradient compensation"}}` | +| DigitizedLandmarks | REQUIRED. Boolean ("true" or "false") value indicating whether anatomical landmark points (i.e. fiducials) are contained within this recording. | +| DigitizedHeadPoints | REQUIRED. Boolean (`true` or `false`) value indicating whether head points outlining the scalp/face surface are contained within this recording. | SHOULD be present -| Field name | Definition | -| :------------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| MEGChannelCount | RECOMMENDED. Number of MEG channels (e.g. 275) | -| MEGREFChannelCount | RECOMMENDED. Number of MEG reference channels (e.g. 23). For systems without such channels (e.g. Neuromag Vectorview), `MEGREFChannelCount`=0 | -| EEGChannelCount | RECOMMENDED. Number of EEG channels recorded simultaneously (e.g. 21) | -| ECOGChannelCount | RECOMMENDED. Number of ECoG channels | -| SEEGChannelCount | RECOMMENDED. Number of SEEG channels | -| EOGChannelCount | RECOMMENDED. Number of EOG channels | -| ECGChannelCount | RECOMMENDED. Number of ECG channels | -| EMGChannelCount | RECOMMENDED. Number of EMG channels | -| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals | -| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers | -| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g. 3600) | -| RecordingType | RECOMMENDED. Defines whether the recording is `continuous` or `epoched`; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) | -| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g. 1) in case of epoched data | -| ContinuousHeadLocalization | RECOMMENDED. Boolean (`true` or `false`) value indicating whether continuous head localisation was performed. | -| HeadCoilFrequency | RECOMMENDED. List of frequencies (in Hz) used by the head localisation coils (‘HLC’ in CTF systems, ‘HPI’ in Elekta, ‘COH’ in BTi/4D) that track the subject’s head position in the MEG helmet (e.g. `[293, 307, 314, 321]`) | -| MaxMovement | RECOMMENDED. Maximum head movement (in mm) detected during the recording, as measured by the head localisation coils (e.g., 4.8) | -| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g. "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. | -| AssociatedEmptyRoom | RECOMMENDED. Relative path in BIDS folder structure to empty-room file associated with the subject’s MEG recording. The path needs to use forward slashes instead of backward slashes (e.g. `sub-emptyroom/ses-/meg/sub-emptyroom_ses-_task-noise_run-_meg.ds`). | -| HardwareFilters | RECOMMENDED. List of temporal hardware filters applied. Ideally key:value pairs of pre-applied hardware filters and their parameter values: e.g., `{"HardwareFilters": {"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}}`. Write `n/a` if no hardware filters applied. | +| Field name | Definition | +| :------------------------- | :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| MEGChannelCount | RECOMMENDED. Number of MEG channels (e.g. 275) | +| MEGREFChannelCount | RECOMMENDED. Number of MEG reference channels (e.g. 23). For systems without such channels (e.g. Neuromag Vectorview), `MEGREFChannelCount`=0 | +| EEGChannelCount | RECOMMENDED. Number of EEG channels recorded simultaneously (e.g. 21) | +| ECOGChannelCount | RECOMMENDED. Number of ECoG channels | +| SEEGChannelCount | RECOMMENDED. Number of SEEG channels | +| EOGChannelCount | RECOMMENDED. Number of EOG channels | +| ECGChannelCount | RECOMMENDED. Number of ECG channels | +| EMGChannelCount | RECOMMENDED. Number of EMG channels | +| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals | +| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers | +| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g. 3600) | +| RecordingType | RECOMMENDED. Defines whether the recording is `continuous` or `epoched`; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) | +| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g. 1) in case of epoched data | +| ContinuousHeadLocalization | RECOMMENDED. Boolean (`true` or `false`) value indicating whether continuous head localisation was performed. | +| HeadCoilFrequency | RECOMMENDED. List of frequencies (in Hz) used by the head localisation coils (‘HLC’ in CTF systems, ‘HPI’ in Elekta, ‘COH’ in BTi/4D) that track the subject’s head position in the MEG helmet (e.g. `[293, 307, 314, 321]`) | +| MaxMovement | RECOMMENDED. Maximum head movement (in mm) detected during the recording, as measured by the head localisation coils (e.g., 4.8) | +| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g. "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. | +| AssociatedEmptyRoom | RECOMMENDED. Relative path in BIDS folder structure to empty-room file associated with the subject’s MEG recording. The path needs to use forward slashes instead of backward slashes (e.g. `sub-emptyroom/ses-/meg/sub-emptyroom_ses-_task-noise_run-_meg.ds`). | +| HardwareFilters | RECOMMENDED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal hardware filters applied, or `"n/a"` if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}` | Specific EEG fields (if recorded with MEG) SHOULD be present: diff --git a/src/04-modality-specific-files/03-electroencephalography.md b/src/04-modality-specific-files/03-electroencephalography.md index 9f044653e9..505daf1fcb 100644 --- a/src/04-modality-specific-files/03-electroencephalography.md +++ b/src/04-modality-specific-files/03-electroencephalography.md @@ -112,33 +112,33 @@ Whenever possible, please avoid using ad hoc wording. Specific EEG fields MUST be present: -| Field name | Definition | -| :----------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| EEGReference | REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "Cz", "CMS"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the \_channels.tsv file. | -| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400). | -| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the EEG instrument (i.e., 50 or 60). | -| SoftwareFilters | REQUIRED. List of temporal software filters applied. Ideally key:value pairs of pre-applied software filters and their parameter values: e.g., `{"Anti-aliasing filter": {"half-amplitude cutoff (Hz)": 500, "Roll-off": "6dB/Octave"}}`. Write `n/a` if no software filters applied. | +| Field name | Definition | +| :----------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| EEGReference | REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "Cz", "CMS"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the \_channels.tsv file. | +| SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400). | +| PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the EEG instrument (i.e., 50 or 60). | +| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Anti-aliasing filter": {"half-amplitude cutoff (Hz)": 500, "Roll-off": "6dB/Octave"}}`. | SHOULD be present: -| Field name | Definition | -| :--------------------------| :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| CapManufacturer | RECOMMENDED. Name of the cap manufacturer (e.g., "EasyCap"). | -| CapManufacturersModelName | RECOMMENDED. Manufacturer's designation of the EEG cap model (e.g., "actiCAP 64 Ch Standard-2"). | -| EEGChannelCount | RECOMMENDED. Number of EEG channels included in the recording (e.g., 128). | -| ECGChannelCount | RECOMMENDED. Number of ECG channels. | -| EMGChannelCount | RECOMMENDED. Number of EMG channels. | -| EOGChannelCount | RECOMMENDED. Number of EOG channels. | -| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. | -| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) trigger. | -| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). | -| RecordingType | RECOMMENDED. Defines whether the recording is `continuous`, `discontinuous` or `epoched`. | -| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. | -| HeadCircumference | RECOMMENDED. Circumference of the participants head, expressed in cm (e.g., 58). | -| EEGPlacementScheme | RECOMMENDED. Placement scheme of EEG electrodes. Either the name of a standardized placement system (e.g., "10-20") or a list of standardized electrode names (e.g., `["Cz", "Pz"]`). | -| EEGGround | RECOMMENDED. Description of the location of the ground electrode (e.g., "placed on right mastoid (M2)"). | -| HardwareFilters | RECOMMENDED. List of temporal hardware filters applied. Ideally key:value pairs of pre-applied hardware filters and their parameter values: e.g., `{"HardwareFilters": {"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}}`. Write `n/a` if no hardware filters applied. | -| SubjectArtefactDescription | RECOMMENDED. Free-form description of the observed subject artifact and its possible cause (e.g., "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. | +| Field name | Definition | +| :--------------------------| :-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| CapManufacturer | RECOMMENDED. Name of the cap manufacturer (e.g., "EasyCap"). | +| CapManufacturersModelName | RECOMMENDED. Manufacturer's designation of the EEG cap model (e.g., "actiCAP 64 Ch Standard-2"). | +| EEGChannelCount | RECOMMENDED. Number of EEG channels included in the recording (e.g., 128). | +| ECGChannelCount | RECOMMENDED. Number of ECG channels. | +| EMGChannelCount | RECOMMENDED. Number of EMG channels. | +| EOGChannelCount | RECOMMENDED. Number of EOG channels. | +| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. | +| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) trigger. | +| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). | +| RecordingType | RECOMMENDED. Defines whether the recording is `continuous`, `discontinuous` or `epoched`. | +| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. | +| EEGGround | RECOMMENDED. Description of the location of the ground electrode (e.g., "placed on right mastoid (M2)"). | +| HeadCircumference | RECOMMENDED. Circumference of the participants head, expressed in cm (e.g., 58). | +| EEGPlacementScheme | RECOMMENDED. Placement scheme of EEG electrodes. Either the name of a standardized placement system (e.g., "10-20") or a list of standardized electrode names (e.g., `["Cz", "Pz"]`). | +| HardwareFilters | RECOMMENDED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal hardware filters applied, or `"n/a"` if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}` | +| SubjectArtefactDescription | RECOMMENDED. Free-form description of the observed subject artifact and its possible cause (e.g., "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to `n/a`, it will be interpreted as absence of major source of artifacts except cardiac and blinks. | Example: @@ -163,6 +163,12 @@ Example: "EEGPlacementScheme":"10 percent system", "EEGReference":"single electrode placed on FCz", "EEGGround":"placed on AFz", + "SoftwareFilters":{ + "Anti-aliasing filter":{ + "half-amplitude cutoff (Hz)": 500, + "Roll-off": "6dB/Octave" + } + }, "HardwareFilters":{ "ADC's decimation filter (hardware bandwidth limit)":{ "-3dB cutoff point (Hz)":480, diff --git a/src/04-modality-specific-files/04-intracranial-electroencephalography.md b/src/04-modality-specific-files/04-intracranial-electroencephalography.md index 77970486a6..9733adceab 100644 --- a/src/04-modality-specific-files/04-intracranial-electroencephalography.md +++ b/src/04-modality-specific-files/04-intracranial-electroencephalography.md @@ -66,7 +66,7 @@ in the sidecar JSON file. Other relevant files MAY be included alongside the original iEEG data in the [`/sourcedata` directory](../02-common-principles.md#source-vs-raw-vs-derived-data). Note the RecordingType, which depends on whether the data stream on disk is interrupted or not. Continuous data is by definition 1 segment without interruption. Epoched data consists of multiple segments that all have the same length (e.g., corresponding to trials) and that have gaps in between. Discontinuous data consists of multiple segments of different length, for example due to a pause in the acquisition. - + ### Terminology: Electrodes vs. Channels For proper documentation of iEEG recording metadata it is important to @@ -130,31 +130,31 @@ Specific iEEG fields MUST be present: | iEEGReference | REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "bipolar", "T01" for electrode with name T01, "intracranial electrode on top of a grid, not included with data", "upside down electrode"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the \_channels.tsv file. | | SamplingFrequency | REQUIRED. Sampling frequency (in Hz) of all the iEEG channels in the recording (e.g., 2400). All other channels should have frequency specified as well in the `channels.tsv` file. | | PowerLineFrequency | REQUIRED. Frequency (in Hz) of the power grid where the iEEG recording was done (i.e., 50 or 60). | -| SoftwareFilters | REQUIRED. List of temporal software filters applied or ideally key:value pairs of pre-applied filters and their parameter values. (n/a if none). E.g., "{'HighPass': {'HalfAmplitudeCutOffHz': 1, 'RollOff: '6dB/Octave'}}". | +| SoftwareFilters | REQUIRED. A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal software filters applied, or `"n/a"` if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"HighPass": {"HalfAmplitudeCutOffHz": 1, "RollOff": "6dB/Octave"}}` | Specific iEEG fields SHOULD be present: -| Field name | Definition | -| :------------------------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| DCOffsetCorrection | RECOMMENDED. A description of the method (if any) used to correct for a DC offset. If the method used was subtracting the mean value for each channel, use "mean". | -| HardwareFilters | RECOMMENDED. List of temporal hardware filters applied. Ideally key:value pairs of pre-applied hardware filters and their parameter values: e.g., `{"HardwareFilters": {"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}}`. Write `n/a` if no hardware filters applied. | -| ElectrodeManufacturer | RECOMMENDED. can be used if all electrodes are of the same manufacturer (e.g., AD-TECH, DIXI). If electrodes of different manufacturers are used, please use the corresponding table in the \_electrodes.tsv file. | -| ElectrodeManufacturersModelName | RECOMMENDED. If different electrode types are used, please use the corresponding table in the \_electrodes.tsv file. | -| ECOGChannelCount | RECOMMENDED. Number of iEEG surface channels included in the recording (e.g., 120). | -| SEEGChannelCount | RECOMMENDED. Number of iEEG depth channels included in the recording (e.g., 8). | -| EEGChannelCount | RECOMMENDED. Number of scalp EEG channels recorded simultaneously (e.g., 21). | -| EOGChannelCount | RECOMMENDED. Number of EOG channels. | -| ECGChannelCount | RECOMMENDED. Number of ECG channels. | -| EMGChannelCount | RECOMMENDED. Number of EMG channels. | -| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. | -| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers. | -| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). | -| RecordingType | RECOMMENDED. Defines whether the recording is "continuous", "discontinuous" or "epoched"; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) | -| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. If recording was continuous or discontinuous, leave out the field. | -| iEEGGround | RECOMMENDED. Description of the location of the ground electrode ("placed on right mastoid (M2)"). | -| iEEGPlacementScheme | RECOMMENDED. Freeform description of the placement of the iEEG electrodes. Left/right/bilateral/depth/surface (e.g., "left frontal grid and bilateral hippocampal depth" or "surface strip and STN depth" or "clinical indication bitemporal, bilateral temporal strips and left grid"). | -| iEEGElectrodeGroups | RECOMMENDED. Field to describe the way electrodes are grouped into strips, grids or depth probes e.g., {'grid1': "10x8 grid on left temporal pole", 'strip2': "1x8 electrode strip on xxx"}. | -| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g., "door open", "nurse walked into room at 2 min", "seizure at 10 min"). If this field is left empty, it will be interpreted as absence of artifacts. | +| Field name | Definition | +| :------------------------------ | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| DCOffsetCorrection | RECOMMENDED. A description of the method (if any) used to correct for a DC offset. If the method used was subtracting the mean value for each channel, use "mean". | +| HardwareFilters | RECOMMENDED.A [JSON object](https://www.w3schools.com/js/js_json_objects.asp) of temporal hardware filters applied, or `"n/a"` if the data is not available. Each key:value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key:value pairs. E.g., `{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}` | +| ElectrodeManufacturer | RECOMMENDED. can be used if all electrodes are of the same manufacturer (e.g., AD-TECH, DIXI). If electrodes of different manufacturers are used, please use the corresponding table in the \_electrodes.tsv file. | +| ElectrodeManufacturersModelName | RECOMMENDED. If different electrode types are used, please use the corresponding table in the \_electrodes.tsv file. | +| ECOGChannelCount | RECOMMENDED. Number of iEEG surface channels included in the recording (e.g., 120). | +| SEEGChannelCount | RECOMMENDED. Number of iEEG depth channels included in the recording (e.g., 8). | +| EEGChannelCount | RECOMMENDED. Number of scalp EEG channels recorded simultaneously (e.g., 21). | +| EOGChannelCount | RECOMMENDED. Number of EOG channels. | +| ECGChannelCount | RECOMMENDED. Number of ECG channels. | +| EMGChannelCount | RECOMMENDED. Number of EMG channels. | +| MiscChannelCount | RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals. | +| TriggerChannelCount | RECOMMENDED. Number of channels for digital (TTL bit level) triggers. | +| RecordingDuration | RECOMMENDED. Length of the recording in seconds (e.g., 3600). | +| RecordingType | RECOMMENDED. Defines whether the recording is "continuous", "discontinuous" or "epoched"; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.) | +| EpochLength | RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. If recording was continuous or discontinuous, leave out the field. | +| iEEGGround | RECOMMENDED. Description of the location of the ground electrode ("placed on right mastoid (M2)"). | +| iEEGPlacementScheme | RECOMMENDED. Freeform description of the placement of the iEEG electrodes. Left/right/bilateral/depth/surface (e.g., "left frontal grid and bilateral hippocampal depth" or "surface strip and STN depth" or "clinical indication bitemporal, bilateral temporal strips and left grid"). | +| iEEGElectrodeGroups | RECOMMENDED. Field to describe the way electrodes are grouped into strips, grids or depth probes e.g., {'grid1': "10x8 grid on left temporal pole", 'strip2': "1x8 electrode strip on xxx"}. | +| SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g., "door open", "nurse walked into room at 2 min", "seizure at 10 min"). If this field is left empty, it will be interpreted as absence of artifacts. | Specific iEEG fields MAY be present: diff --git a/src/04-modality-specific-files/05-task-events.md b/src/04-modality-specific-files/05-task-events.md index 35a9e751ec..5d35a72040 100644 --- a/src/04-modality-specific-files/05-task-events.md +++ b/src/04-modality-specific-files/05-task-events.md @@ -20,7 +20,7 @@ recorded during the scan. Events MAY be either stimuli presented to the participant or participant responses. A single event file MAY include any combination of stimuli and response events. Events MAY overlap in time. Please mind that this does not imply that only so called "event related" study designs -are supported (in contract to "block" designs) - each "block of events" can be +are supported (in contrast to "block" designs) - each "block of events" can be represented by an individual row in the \_events.tsv file (with a long duration). Each task events file REQUIRES a corresponding task imaging data file (but a single events file MAY be shared by multiple imaging data files - see diff --git a/src/99-appendices/08-coordinate-systems.md b/src/99-appendices/08-coordinate-systems.md index 8046c1b793..c243f5640a 100644 --- a/src/99-appendices/08-coordinate-systems.md +++ b/src/99-appendices/08-coordinate-systems.md @@ -123,32 +123,38 @@ the units are assumed to be mm. | individual | Participant specific anatomical space (for example derived from T1w and/or T2w images). This coordinate system requires specifying an additional, participant-specific file to be fully defined. In context of surfaces this space has been refered to as `fsnative`. | | custom | Custom space defined using a group/study-specific template. This coordinate system requires specifying an additional file to be fully defined. | -### Volume - -| Coordinate System | Description | -| --------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| FS305 | FreeSurfer variant of the MNI305 space | -| MNI152Lin | Also known as ICBM (version with linear coregistration) [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin) | -| MNI152NLin6\[Sym|Asym\] | Also known as ICBM 6th generation (non-linear coregistration). Used by SPM99 - SPM8 and FSL (MNI152NLin6Sym). [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6) | -| MNI152NLin6AsymConte69 | Template based on MNI152NLin6Asym using Conte69 data. Built by Human Connectome Project. [https://github.com/Washington-University/HCPpipelines/tree/master/global/templates](https://github.com/Washington-University/HCPpipelines/tree/master/global/templates) | -| MNI152NLin2009\[a-c\]\[Sym|Asym\] | Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). It comes in either three different flavours each in symmetric or asymmetric version. [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) | -| MNIColin27 | Average of 27 T1 scans of a single subject [http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres](http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres) | -| MNI305 | Also known as avg305. | -| NIHPD | Pediatric templates generated from the NIHPD sample. Available for different age groups (4.5–18.5 y.o., 4.5–8.5 y.o., 7–11 y.o., 7.5–13.5 y.o., 10–14 y.o., 13–18.5 y.o. This template also comes in either -symmetric or -asymmetric flavor. [http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1](http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1) | -| Talairach | Piecewise linear scaling of the brain is implemented as described in TT88. [http://www.talairach.org/](http://www.talairach.org/) | -| OASIS30AntsOASISAnts | [https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436](https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436) | -| OASIS30Atropos | [https://mindboggle.info/data.html](https://mindboggle.info/data.html) | -| ICBM452AirSpace | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation" [https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf](https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf) | -| ICBM452Warp5Space | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" [https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf](https://www.loni.usc.edu/docs/atlases_methods/ICBM_452_T1_Atlas_Methods.pdf) | -| IXI549Space | Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452.Used by SPM12. [http://www.brain-development.org/](http://www.brain-development.org/) | -| UNCInfant\[0|1|2\]V\[21|22|23\] | Infant Brain Atlases from Neonates to 1- and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas) | - -### Surface - -| Coordinate System | Description | -| -------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| fsaverage\[3|4|5|6|sym\] | Images were sampled to the FreeSurfer surface reconstructed from the subject’s T1w image, and registered to an fsaverage template | -| fsLR\[164k|59k|32k|4k\] | Images were sampled to the 164k (used by HCP pipelines for 3T and 7T anatomical analysis), 59k (used by HCP pipelines for 7T MRI bold and DWI analysis), 32k (used by HCP pipelines for 3T MRI bold and DWI analysis), or 4k (used by HCP pipelines for MEG analysis) fsaverage_LR surface reconstructed from the T1w image | +### Standard template identifiers + +| Coordinate System | Description | +| --------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| FS305 | FreeSurfer variant of the MNI305 space | +| ICBM452AirSpace | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation" [https://www.loni.usc.edu/research/atlases](https://www.loni.usc.edu/research/atlases) | +| ICBM452Warp5Space | Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" [https://www.loni.usc.edu/research/atlases](https://www.loni.usc.edu/research/atlases) | +| IXI549Space | Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452. Used by SPM12. [http://www.brain-development.org/](http://www.brain-development.org/) | +| fsaverage\[|Sym\] | The `fsaverage` is a **dual template** providing both volumetric and surface coordinates references. The volumetric template corresponds to a FreeSurfer variant of `MNI305` space. The `fsaverage` atlas also defines a surface reference system (formerly described as fsaverage\[3|4|5|6|sym\]). The `fsaverageSym` is the symmetric counterpart of `fsaverage`. | +| fsLR | The `fsLR` is a **dual template** providing both volumetric and surface coordinates references. The volumetric template corresponds to `MNI152NLin6Asym`. Surface templates are given at several sampling densities: 164k (used by HCP pipelines for 3T and 7T anatomical analysis), 59k (used by HCP pipelines for 7T MRI bold and DWI analysis), 32k (used by HCP pipelines for 3T MRI bold and DWI analysis), or 4k (used by HCP pipelines for MEG analysis) fsaverage_LR surface reconstructed from the T1w image. | +| MNIColin27 | Average of 27 T1 scans of a single subject [http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres](http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres) | +| MNI152Lin | Also known as ICBM (version with linear coregistration) [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin) | +| MNI152NLin2009\[a-c\]\[Sym|Asym\] | Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). It comes in either three different flavours each in symmetric or asymmetric version. [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) | +| MNI152NLin6Sym | Also known as symmetric ICBM 6th generation (non-linear coregistration). Used by SPM99 - SPM8. [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6) | +| MNI152NLin6Asym | A variation of `MNI152NLin6Sym` built by A. Janke that is released as the *MNI template* of FSL. Volumetric templates included with [HCP-Pipelines](https://github.com/Washington-University/HCPpipelines/tree/master/global/templates) correspond to this template too. See [10.1016/j.neuroimage.2012.01.024](https://doi.org/10.1016/j.neuroimage.2012.01.024). | +| MNI152NLin6AsymConte69 | Template based on MNI152NLin6Asym using Conte69 data. Built by Human Connectome Project. [https://github.com/Washington-University/HCPpipelines/tree/master/global/templates](https://github.com/Washington-University/HCPpipelines/tree/master/global/templates) | +| MNI305 | Also known as avg305. | +| NIHPD\[Sym|Asym\] | Pediatric templates generated from the NIHPD sample. Available for different age groups (4.5–18.5 y.o., 4.5–8.5 y.o., 7–11 y.o., 7.5–13.5 y.o., 10–14 y.o., 13–18.5 y.o. This template also comes in either -symmetric or -asymmetric flavor. [http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1](http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1) | +| OASIS30AntsOASISAnts | [https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436](https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436) | +| OASIS30Atropos | [https://mindboggle.info/data.html](https://mindboggle.info/data.html) | +| Talairach | Piecewise linear scaling of the brain is implemented as described in TT88. [http://www.talairach.org/](http://www.talairach.org/) | +| UNCInfant | Infant Brain Atlases from Neonates to 1- and 2-year-olds. [https://www.nitrc.org/projects/pediatricatlas](https://www.nitrc.org/projects/pediatricatlas) | + +The following template identifiers are retained for backwards compatibility +of BIDS implementations. +Their use is NOT RECOMMENDED for new BIDS datasets and tooling, but their +presence MUST NOT produce a validation error. + +| Coordinate System | Recommended identifier | +| --------------------------------------------------- | ---------------------- | +| fsaverage\[3|4|5|6|sym\] | fsaverage\[|Sym\] | +| UNCInfant\[0|1|2\]V\[21|22|23\] | UNCInfant | ### Hybrid (Volume/Surface) aliases diff --git a/src/CHANGES.md b/src/CHANGES.md index 7e33a5d03b..05c197e47b 100644 --- a/src/CHANGES.md +++ b/src/CHANGES.md @@ -2,13 +2,18 @@ Changelog ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD) +- specify further the pipeline following #345 [#358](https://github.com/bids-standard/bids-specification/pull/358) ([CPernet](https://github.com/CPernet)) +- FIX: clarify that filters should be specified as object of objects [#348](https://github.com/bids-standard/bids-specification/pull/348) ([sappelhoff](https://github.com/sappelhoff)) +- \[FIX] Typo fix (contract -> contrast) in events documentation [#346](https://github.com/bids-standard/bids-specification/pull/346) ([snastase](https://github.com/snastase)) - \[MISC] Move the PR template to a separate folder and improve contents [#338](https://github.com/bids-standard/bids-specification/pull/338) ([jhlegarreta](https://github.com/jhlegarreta)) - \[INFRA] Find npm requirements file in Circle [#336](https://github.com/bids-standard/bids-specification/pull/336) ([franklin-feingold](https://github.com/franklin-feingold)) +- ENH: Clarify the position toward non-compliant derivative datasets and files [#334](https://github.com/bids-standard/bids-specification/pull/334) ([effigies](https://github.com/effigies)) - \[ENH] Clarify phenotypic and assessment data in new section [#331](https://github.com/bids-standard/bids-specification/pull/331) ([sappelhoff](https://github.com/sappelhoff)) - \[MISC] add information about continuous integration checks to PR template [#330](https://github.com/bids-standard/bids-specification/pull/330) ([sappelhoff](https://github.com/sappelhoff)) - \[FIX] Fix `Common principles` `Key/value files` section level [#328](https://github.com/bids-standard/bids-specification/pull/328) ([jhlegarreta](https://github.com/jhlegarreta)) - \[INFRA] Set the maximum heading length lint check to `false` [#325](https://github.com/bids-standard/bids-specification/pull/325) ([jhlegarreta](https://github.com/jhlegarreta)) - \[FIX] Number explicitly all cases in MRI field map section headers [#323](https://github.com/bids-standard/bids-specification/pull/323) ([jhlegarreta](https://github.com/jhlegarreta)) +- \[FIX] Add SoftwareFilters to EEG sidecar example [#322](https://github.com/bids-standard/bids-specification/pull/322) ([Remi-Gau](https://github.com/Remi-Gau)) - \[MISC] Fixing Travis errors with Remark [#320](https://github.com/bids-standard/bids-specification/pull/320) ([franklin-feingold](https://github.com/franklin-feingold)) - \[INFRA] Link to doc builds in CI checks [#315](https://github.com/bids-standard/bids-specification/pull/315) ([jasmainak](https://github.com/jasmainak)) - \[MISC] Add BEP027 - BIDS Execution to BEP list [#314](https://github.com/bids-standard/bids-specification/pull/314) ([effigies](https://github.com/effigies))