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[MISC] Update all links to use HTTPS whenever possible. (#676)
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* Update all links to use HTTPS whenever possible.

* Simplify inclusion of links within sentences

* Update src/04-modality-specific-files/02-magnetoencephalography.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/02-licenses.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* Update src/99-appendices/08-coordinate-systems.md

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* fix links and table pipes

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
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13 changes: 7 additions & 6 deletions src/02-common-principles.md
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Expand Up @@ -429,7 +429,7 @@ acquisition parameters available in DICOM files, we RECOMMEND that users provide
additional meta information extracted from DICOM files in a sidecar JSON file
(with the same filename as the `.nii[.gz]` file, but with a `.json` extension).
Extraction of BIDS compatible metadata can be performed using [dcm2niix](https://github.com/rordenlab/dcm2niix)
and [dicm2nii](http://www.mathworks.com/matlabcentral/fileexchange/42997-dicom-to-nifti-converter/content/dicm2nii.m)
and [dicm2nii](https://www.mathworks.com/matlabcentral/fileexchange/42997-xiangruili-dicm2nii)
DICOM to NIfTI converters. The [BIDS-validator](https://github.com/bids-standard/bids-validator)
will check for conflicts between the JSON file and the data recorded in the
NIfTI header.
Expand Down Expand Up @@ -504,7 +504,7 @@ Example:
"bmi": {
"LongName": "Body mass index",
"Units": "kg/m^2",
"TermURL": "http://purl.bioontology.org/ontology/SNOMEDCT/60621009"
"TermURL": "https://purl.bioontology.org/ontology/SNOMEDCT/60621009"
}
}
```
Expand All @@ -513,10 +513,11 @@ Example:

JavaScript Object Notation (JSON) files MUST be used for storing key/value
pairs. JSON files MUST be in UTF-8 encoding. Extensive documentation of the
format can be found here: [http://json.org/](http://json.org/). Several editors
have built-in support for JSON syntax highlighting that aids manual creation of
such files. An online editor for JSON with built-in validation is available at:
[http://jsoneditoronline.org](http://jsoneditoronline.org).
format can be found at [https://www.json.org/](https://www.json.org/).
Several editors have built-in support for JSON syntax highlighting that aids
manual creation of such files.
An online editor for JSON with built-in validation is available at
[https://jsoneditoronline.org](https://jsoneditoronline.org).
It is RECOMMENDED that keys in a JSON file are written in [CamelCase](https://en.wikipedia.org/wiki/Camel_case)
with the first letter in upper case (for example, `SamplingFrequency`, not
`samplingFrequency`). Note however, when a JSON file is used as an accompanying
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2 changes: 1 addition & 1 deletion src/03-modality-agnostic-files.md
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Expand Up @@ -292,7 +292,7 @@ As an example, consider the contents of a file called
{
"MeasurementToolMetadata": {
"Description": "Adult ADHD Clinical Diagnostic Scale V1.2",
"TermURL": "http://www.cognitiveatlas.org/task/id/trm_5586ff878155d"
"TermURL": "https://www.cognitiveatlas.org/task/id/trm_5586ff878155d"
},
"adhd_b": {
"Description": "B. CHILDHOOD ONSET OF ADHD (PRIOR TO AGE 7)",
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24 changes: 12 additions & 12 deletions src/04-modality-specific-files/02-magnetoencephalography.md
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Expand Up @@ -91,18 +91,18 @@ SHOULD be present: For consistency between studies and institutions, we
encourage users to extract the values of these fields from the actual raw data.
Whenever possible, please avoid using ad-hoc wording.

| **Key name** | **Requirement level** | **Data type** | **Description** |
|------------------------|-----------------------|---------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| InstitutionName | RECOMMENDED | [string][] | The name of the institution in charge of the equipment that produced the composite instances. |
| InstitutionAddress | RECOMMENDED | [string][] | The address of the institution in charge of the equipment that produced the composite instances. |
| Manufacturer | RECOMMENDED | [string][] | Manufacturer of the MEG system (`CTF`, `Elekta/Neuromag`, `BTi/4D`, `KIT/Yokogawa`, `ITAB`, `KRISS`, `Other`). See [Appendix VII](../99-appendices/07-meg-systems.md) with preferred names. |
| ManufacturersModelName | RECOMMENDED | [string][] | Manufacturer’s designation of the MEG scanner model (for example, `CTF-275`). See [Appendix VII](../99-appendices/07-meg-systems.md) with preferred names. |
| SoftwareVersions | RECOMMENDED | [string][] | Manufacturer’s designation of the acquisition software. |
| TaskDescription | RECOMMENDED | [string][] | Description of the task. |
| Instructions | RECOMMENDED | [string][] | Text of the instructions given to participants before the scan. This is not only important for behavioral or cognitive tasks but also in resting state paradigms (for example, to distinguish between eyes open and eyes closed). |
| CogAtlasID | RECOMMENDED | [string][] | [URI][uri] of the corresponding [Cognitive Atlas](http://www.cognitiveatlas.org/) term that describes the task (for example, Resting State with eyes closed "[http://www.cognitiveatlas.org/task/id/trm_54e69c642d89b](http://www.cognitiveatlas.org/task/id/trm_54e69c642d89b)"). |
| CogPOID | RECOMMENDED | [string][] | [URI][uri] of the corresponding [CogPO](http://www.cogpo.org/) term that describes the task (for example, Rest "[http://wiki.cogpo.org/index.php?title=Rest](http://wiki.cogpo.org/index.php?title=Rest)"). |
| DeviceSerialNumber | RECOMMENDED | [string][] | The serial number of the equipment that produced the composite instances. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset. |
| **Key name** | **Requirement level** | **Data type** | **Description** |
|------------------------|-----------------------|---------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| InstitutionName | RECOMMENDED | [string][] | The name of the institution in charge of the equipment that produced the composite instances. |
| InstitutionAddress | RECOMMENDED | [string][] | The address of the institution in charge of the equipment that produced the composite instances. |
| Manufacturer | RECOMMENDED | [string][] | Manufacturer of the MEG system (`CTF`, `Elekta/Neuromag`, `BTi/4D`, `KIT/Yokogawa`, `ITAB`, `KRISS`, `Other`). See [Appendix VII](../99-appendices/07-meg-systems.md) with preferred names. |
| ManufacturersModelName | RECOMMENDED | [string][] | Manufacturer’s designation of the MEG scanner model (for example, `CTF-275`). See [Appendix VII](../99-appendices/07-meg-systems.md) with preferred names. |
| SoftwareVersions | RECOMMENDED | [string][] | Manufacturer’s designation of the acquisition software. |
| TaskDescription | RECOMMENDED | [string][] | Description of the task. |
| Instructions | RECOMMENDED | [string][] | Text of the instructions given to participants before the scan. This is not only important for behavioral or cognitive tasks but also in resting state paradigms (for example, to distinguish between eyes open and eyes closed). |
| CogAtlasID | RECOMMENDED | [string][] | [URI][uri] of the corresponding [Cognitive Atlas](https://www.cognitiveatlas.org/) term that describes the task (for example, Resting State with eyes closed "[https://www.cognitiveatlas.org/task/id/trm_54e69c642d89b](https://www.cognitiveatlas.org/task/id/trm_54e69c642d89b)"). |
| CogPOID | RECOMMENDED | [string][] | [URI][uri] of the corresponding [CogPO](http://www.cogpo.org/) term that describes the task (for example, Rest "[http://wiki.cogpo.org/index.php?title=Rest](http://wiki.cogpo.org/index.php?title=Rest)"). |
| DeviceSerialNumber | RECOMMENDED | [string][] | The serial number of the equipment that produced the composite instances. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset. |

Specific MEG fields MUST be present:

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