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[ENH] Add Sources link to all raw datatypes sidecar JSON #906

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[ENH] Add Sources link to all raw datatypes sidecar JSON #906

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534053d
Add RawSources
adam2392 Oct 21, 2021
bf54d1f
Adding to all datatypes
adam2392 Oct 21, 2021
5e0f0eb
Adding to all datatypes
adam2392 Oct 21, 2021
7cd3668
Add changelog
adam2392 Oct 21, 2021
7160c56
Adding updated array
adam2392 Oct 21, 2021
a68699c
Fix CHANGE
adam2392 Oct 22, 2021
047deb2
Adding table for clarification
adam2392 Oct 26, 2021
a4cd06e
Update src/CHANGES.md
adam2392 Oct 26, 2021
ec898a3
Adding to scans
adam2392 Nov 1, 2021
d9b5123
Merge branch 'master' into sources
adam2392 Nov 4, 2021
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12 changes: 7 additions & 5 deletions src/03-modality-agnostic-files.md
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Expand Up @@ -452,6 +452,8 @@ For example, the [EDF](https://www.edfplus.info/)
data format can only contain recording dates after 1985.
Shifting dates is RECOMMENDED, but not required.

The source file path of each recording is also OPTIONAL and can be stored under the ``sources`` column. Similar to [derivatives](./05-derivatives/02-common-data-types.md), it is OPTIONAL to include ``sources``, specifying the filename(s) of the source file used to generate this dataset. If the filename(s) contains patient identifiable information, then it should not be stored.
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double backticks render code in RST, but for MD, it's single backticks 😉

Also: the files under the filename column are relative to the scans.tsv file (this is implicit unfortunately, but relatively clear from the context that this is meant by the text on line 435). --> What should the files under the sources column be relative to? ... should we wait for #918 and make this BIDS-URIs? ... or should it be relative to the dataset root - as you seem to do in your current example?


Additional fields can include external behavioral measures relevant to the
scan.
For example vigilance questionnaire score administered after a resting
Expand All @@ -463,11 +465,11 @@ All such included additional fields SHOULD be documented in an accompanying
Example `_scans.tsv`:

```Text
filename acq_time
func/sub-control01_task-nback_bold.nii.gz 1877-06-15T13:45:30
func/sub-control01_task-motor_bold.nii.gz 1877-06-15T13:55:33
meg/sub-control01_task-rest_split-01_meg.nii.gz 1877-06-15T12:15:27
meg/sub-control01_task-rest_split-02_meg.nii.gz 1877-06-15T12:15:27
filename acq_time sources
func/sub-control01_task-nback_bold.nii.gz 1877-06-15T13:45:30 sourcedata/sub01/dicoms
func/sub-control01_task-motor_bold.nii.gz 1877-06-15T13:55:33 sourcedata/sub01/motordicoms
meg/sub-control01_task-rest_split-01_meg.nii.gz 1877-06-15T12:15:27 sourcedata/sub01/restdicoms
meg/sub-control01_task-rest_split-02_meg.nii.gz 1877-06-15T12:15:27 sourcedata/sub01/restdicoms2
```

## Sessions file
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10 changes: 10 additions & 0 deletions src/04-modality-specific-files/01-magnetic-resonance-imaging-data.md
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Expand Up @@ -188,6 +188,16 @@ When adding additional metadata please use the CamelCase version of
whenever possible. See also
[recommendations on JSON files](../02-common-principles.md#keyvalue-files-dictionaries).

### Source Filename

Similar to [derivatives](../05-derivatives/02-common-data-types.md), it is OPTIONAL to include ``Sources`` as a key in the sidecar JSON, specifying the filename(s) of the source file used to generate this dataset. If the filename(s) contains patient identifiable information, then it should not be stored in ``Sources``.

{{ MACROS___make_metadata_table(
{
"Sources": ("OPTIONAL", "URI of source file used to generate the current file. Care should be taken not to leak patient identifiable information for publicly shared datasets.")
}
) }}

## Anatomy imaging data

{{ MACROS___make_filename_template(datatypes=["anat"]) }}
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11 changes: 10 additions & 1 deletion src/04-modality-specific-files/02-magnetoencephalography.md
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Expand Up @@ -169,6 +169,14 @@ SHOULD be present:
}
) }}

Similar to [derivatives](../05-derivatives/02-common-data-types.md), it is OPTIONAL to include ``Sources`` as a key in the sidecar JSON, specifying the filename(s) of the source file used to generate this dataset. If the filename(s) contains patient identifiable information, then it should not be stored in ``Sources``.

{{ MACROS___make_metadata_table(
{
"Sources": ("OPTIONAL", "URI of source file used to generate the current file. Care should be taken not to leak patient identifiable information for publicly shared datasets.")
}
) }}

Example:

```JSON
Expand Down Expand Up @@ -198,7 +206,8 @@ Example:
"ContinuousHeadLocalization": true,
"HeadCoilFrequency": [1470,1530,1590],
"DigitizedLandmarks": true,
"DigitizedHeadPoints": true
"DigitizedHeadPoints": true,
"Sources": ["001-upright-meg.ds"],
}
```

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11 changes: 10 additions & 1 deletion src/04-modality-specific-files/03-electroencephalography.md
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Expand Up @@ -148,6 +148,14 @@ SHOULD be present:
}
) }}

Similar to [derivatives](../05-derivatives/02-common-data-types.md), it is OPTIONAL to include ``Sources`` as a key in the sidecar JSON, specifying the filename(s) of the source file used to generate this dataset. If the filename(s) contains patient identifiable information, then it should not be stored in ``Sources``.

{{ MACROS___make_metadata_table(
{
"Sources": ("OPTIONAL", "URI of source file used to generate the current file. Care should be taken not to leak patient identifiable information for publicly shared datasets.")
}
) }}

Example:

```JSON
Expand Down Expand Up @@ -184,7 +192,8 @@ Example:
}
},
"RecordingDuration":600,
"RecordingType":"continuous"
"RecordingType":"continuous",
"Sources": ["001-eeg-recording.vhdr"]
}
```

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11 changes: 10 additions & 1 deletion src/04-modality-specific-files/04-intracranial-electroencephalography.md
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Expand Up @@ -167,6 +167,14 @@ Specific iEEG fields MAY be present:
}
) }}

Similar to [derivatives](../05-derivatives/02-common-data-types.md), it is OPTIONAL to include ``Sources`` as a key in the sidecar JSON, specifying the filename(s) of the source file used to generate this dataset. If the filename(s) contains patient identifiable information, then it should not be stored in ``Sources``.

{{ MACROS___make_metadata_table(
{
"Sources": ("OPTIONAL", "URI of source file used to generate the current file. Care should be taken not to leak patient identifiable information for publicly shared datasets.")
}
) }}

Example:

```JSON
Expand Down Expand Up @@ -196,7 +204,8 @@ Example:
"RecordingType":"continuous",
"iEEGGround":"placed on the right mastoid",
"iEEGPlacementScheme":"right occipital temporal surface",
"ElectricalStimulation":false
"ElectricalStimulation":false,
"Sources": ["001-visual.edf"]
}
```

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7 changes: 7 additions & 0 deletions src/04-modality-specific-files/06-physiological-and-other-continuous-recordings.md
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Expand Up @@ -158,4 +158,11 @@ of any `*_<physio>.tsv.gz` file.
}
) }}

Similar to [derivatives](../05-derivatives/02-common-data-types.md), it is OPTIONAL to include ``Sources`` as a key in the sidecar JSON, specifying the filename(s) of the source file used to generate this dataset. If the filename(s) contains patient identifiable information, then it should not be stored in ``Sources``.

{{ MACROS___make_metadata_table(
{
"Sources": ("OPTIONAL", "URI of source file used to generate the current file. Care should be taken not to leak patient identifiable information for publicly shared datasets.")
}
) }}
<!-- Link Definitions -->
3 changes: 3 additions & 0 deletions src/04-modality-specific-files/07-behavioral-experiments.md
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Expand Up @@ -31,6 +31,8 @@ In addition of the metadata REQUIRED for some data that can be found in the `beh
(for example `SamplingFrequency` and `StartTime` for `*_<physio|stim>.tsv.gz` files),
it is RECOMMENDED to add the following metadata to the JSON files of this folder.

Similar to [derivatives](../05-derivatives/02-common-data-types.md), it is OPTIONAL to include ``Sources`` as a key in the sidecar JSON, specifying the filename(s) of the source file used to generate this dataset. If the filename(s) contains patient identifiable information, then it should not be stored in ``Sources``.

{{ MACROS___make_metadata_table(
{
"TaskName": "RECOMMENDED",
Expand All @@ -41,5 +43,6 @@ it is RECOMMENDED to add the following metadata to the JSON files of this folder
"InstitutionName": "RECOMMENDED",
"InstitutionAddress": "RECOMMENDED",
"InstitutionalDepartmentName": "RECOMMENDED",
"Sources": ("OPTIONAL", "URI of source file used to generate the current file. Care should be taken not to leak patient identifiable information for publicly shared datasets.")
}
) }}
13 changes: 12 additions & 1 deletion src/04-modality-specific-files/09-positron-emission-tomography.md
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Expand Up @@ -235,6 +235,16 @@ We refer to the common principles for the standards for describing dates and tim

All reconstruction-specific parameters that are not specified, but one wants to include, should go into the `ReconMethodParameterValues` field.

#### Source Filename

Similar to [derivatives](../05-derivatives/02-common-data-types.md), it is OPTIONAL to include ``Sources`` as a key in the sidecar JSON, specifying the filename(s) of the source file used to generate this dataset. If the filename(s) contains patient identifiable information, then it should not be stored in ``Sources``.

{{ MACROS___make_metadata_table(
{
"Sources": ("OPTIONAL", "URI of source file used to generate the current file. Care should be taken not to leak patient identifiable information for publicly shared datasets.")
}
) }}

#### Example (`*_pet.json`)

```JSON
Expand Down Expand Up @@ -270,7 +280,8 @@ All reconstruction-specific parameters that are not specified, but one wants to
"ReconMethodParameterUnits": ["none","none"],
"ReconMethodParameterValues": [16,10],
"ReconFilterType": "none",
"AttenuationCorrection": "[137Cs]transmission scan-based"
"AttenuationCorrection": "[137Cs]transmission scan-based",
"Sources": ["pet_file.nii"]
}
```

Expand Down