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[FIX] Update links that threw warning in CI #1620

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Sep 29, 2023
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[FIX] Update links that threw warning in CI #1620

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b58cd94
fix some links
Remi-Gau Sep 26, 2023
95ca8ce
fix more links
Remi-Gau Sep 26, 2023
465364f
fix moe links
Remi-Gau Sep 26, 2023
f2950eb
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 26, 2023
ea0e379
add line break
Remi-Gau Sep 26, 2023
97947d8
format
Remi-Gau Sep 26, 2023
a0e55f0
Apply suggestions from code review
Remi-Gau Sep 29, 2023
0e17de4
fix a few more 'bare' links
Remi-Gau Sep 29, 2023
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2 changes: 1 addition & 1 deletion mkdocs.yml
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Expand Up @@ -42,7 +42,7 @@ nav:
- Cross modality correspondence: appendices/cross-modality-correspondence.md
- Changelog: CHANGES.md
- The BIDS Starter Kit:
- Website: https://bids-standard.github.io/bids-starter-kit
- Website: https://bids-standard.github.io/bids-starter-kit/
- Tutorials: https://bids-standard.github.io/bids-starter-kit/tutorials/tutorials.html
- GitHub repository: https://github.com/bids-standard/bids-starter-kit
theme:
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38 changes: 19 additions & 19 deletions src/appendices/coordinate-systems.md
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2 changes: 1 addition & 1 deletion src/appendices/hed.md
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Expand Up @@ -14,7 +14,7 @@ Individual terms are comma-separated and may be grouped using parentheses to ind
association.
See [https://www.hedtags.org/display_hed.html](https://www.hedtags.org/display_hed.html)
to view the HED schema and the
[HED resources](https://www.hed-resources.org) site for additional information.
[HED resources](https://www.hed-resources.org/en/latest/) site for additional information.

Starting with HED version 8.0.0, HED allows users to annotate using individual
terms or partial paths in the HED vocabulary (for example `Red` or `Visual-presentation`)
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8 changes: 4 additions & 4 deletions src/appendices/meg-file-formats.md
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Expand Up @@ -58,7 +58,7 @@ A guide for using macros can be found at
) }}

To learn more about CTF’s data organization:
[https://www.fieldtriptoolbox.org/getting_started/ctf](https://www.fieldtriptoolbox.org/getting_started/ctf)
[https://www.fieldtriptoolbox.org/getting_started/ctf](https://www.fieldtriptoolbox.org/getting_started/ctf/)

## Neuromag/Elekta/MEGIN

Expand Down Expand Up @@ -235,8 +235,8 @@ A guide for using macros can be found at

More information can be found under the following links:

- [Neuromag/Elekta/MEGIN data organization](https://www.fieldtriptoolbox.org/getting_started/neuromag)
- [BabyMEG](https://www.fieldtriptoolbox.org/getting_started/babysquid)
- [Neuromag/Elekta/MEGIN data organization](https://www.fieldtriptoolbox.org/getting_started/neuromag/)
- [BabyMEG](https://www.fieldtriptoolbox.org/getting_started/babysquid/)

### Recording dates in `.fif` files

Expand Down Expand Up @@ -302,7 +302,7 @@ A guide for using macros can be found at
) }}

More about the 4D neuroimaging/BTi data organization at:
[https://www.fieldtriptoolbox.org/getting_started/bti](https://www.fieldtriptoolbox.org/getting_started/bti)
[https://www.fieldtriptoolbox.org/getting_started/bti](https://www.fieldtriptoolbox.org/getting_started/bti/)

## KIT/Yokogawa/Ricoh

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4 changes: 2 additions & 2 deletions src/introduction.md
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Expand Up @@ -175,7 +175,7 @@ For example:
### Research Resource Identifier (RRID)

BIDS has also a
[Research Resource Identifier (RRID)](https://www.force11.org/group/resource-identification-initiative),
[Research Resource Identifier (RRID)](https://force11.org/group/resource-identification-initiative),
which you can also include in your citations in addition to relevant publications (see above):

- [`RRID:SCR_016124`](https://scicrunch.org/resources/Any/search?q=SCR_016124&l=SCR_016124)
- [`RRID:SCR_016124`](https://scicrunch.org/resources/data/record/nlx_144509-1/SCR_016124/resolver?q=SCR_016124)
6 changes: 3 additions & 3 deletions src/modality-specific-files/electroencephalography.md
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Expand Up @@ -33,7 +33,7 @@ stored in one of the following formats:
| ------------------------------------------------- | ------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| [European data format](https://www.edfplus.info/) | `.edf` | Each recording consists of a single `.edf` file. [`edf+`](https://www.edfplus.info/specs/edfplus.html) files are permitted. The capital `.EDF` extension MUST NOT be used. |
| [BrainVision Core Data Format][bvformat] | `.vhdr`, `.vmrk`, `.eeg` | Each recording consists of a `.vhdr`, `.vmrk`, `.eeg` file triplet. |
| [EEGLAB](https://sccn.ucsd.edu/eeglab) | `.set`, `.fdt` | The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab). Each recording consists of a `.set` file with an OPTIONAL `.fdt` file. |
| [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php) | `.set`, `.fdt` | The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php). Each recording consists of a `.set` file with an OPTIONAL `.fdt` file. |
| [Biosemi](https://www.biosemi.com/) | `.bdf` | Each recording consists of a single `.bdf` file. [`bdf+`](https://www.teuniz.net/edfbrowser/bdfplus%20format%20description.html) files are permitted. The capital `.BDF` extension MUST NOT be used. |

It is RECOMMENDED to use the European data format, or the BrainVision data
Expand Down Expand Up @@ -359,10 +359,10 @@ triangulate the position of other LED-lit electrodes on a research subject's
head.

- For more information on the definition of anatomical landmarks, please visit:
[https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined)
[https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined/)
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- For more information on coordinate systems for coregistration, please visit:
[https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined)
[https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined/)
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General fields:

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14 changes: 7 additions & 7 deletions src/modality-specific-files/intracranial-electroencephalography.md
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Expand Up @@ -29,13 +29,13 @@ The iEEG community uses a variety of formats for storing raw data, and there is
no single standard that all researchers agree on. For BIDS, iEEG data MUST be
stored in one of the following formats:

| **Format** | **Extension(s)** | **Description** |
| -------------------------------------------------------------- | ------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| [European data format](https://www.edfplus.info/) | `.edf` | Each recording consists of a `.edf` single file. [`edf+`](https://www.edfplus.info/specs/edfplus.html) files are permitted. The capital `.EDF` extension MUST NOT be used. |
| [BrainVision Core Data Format][bvformat] | `.vhdr`, `.vmrk`, `.eeg` | Each recording consists of a `.vhdr`, `.vmrk`, `.eeg` file triplet. |
| [EEGLAB](https://sccn.ucsd.edu/eeglab) | `.set`, `.fdt` | The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab). Each recording consists of a `.set` file with an OPTIONAL `.fdt` file. |
| [Neurodata Without Borders](https://nwb-schema.readthedocs.io) | `.nwb` | Each recording consists of a single `.nwb` file. |
| [MEF3](https://osf.io/e3sf9/) | `.mefd` | Each recording consists of a `.mefd` directory. |
| **Format** | **Extension(s)** | **Description** |
| ------------------------------------------------------------------------- | ------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| [European data format](https://www.edfplus.info/) | `.edf` | Each recording consists of a `.edf` single file. [`edf+`](https://www.edfplus.info/specs/edfplus.html) files are permitted. The capital `.EDF` extension MUST NOT be used. |
| [BrainVision Core Data Format][bvformat] | `.vhdr`, `.vmrk`, `.eeg` | Each recording consists of a `.vhdr`, `.vmrk`, `.eeg` file triplet. |
| [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php) | `.set`, `.fdt` | The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php). Each recording consists of a `.set` file with an OPTIONAL `.fdt` file. |
| [Neurodata Without Borders](https://nwb-schema.readthedocs.io/en/latest/) | `.nwb` | Each recording consists of a single `.nwb` file. |
| [MEF3](https://osf.io/e3sf9/) | `.mefd` | Each recording consists of a `.mefd` directory. |

It is RECOMMENDED to use the European data format, or the BrainVision data
format. It is furthermore discouraged to use the other accepted formats over
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2 changes: 1 addition & 1 deletion src/modality-specific-files/magnetic-resonance-imaging-data.md
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Expand Up @@ -9,7 +9,7 @@ MRI acquisition parameters are divided into several categories based on
([article](https://doi.org/10.15200/winn.143191.17127)) by Ben Inglis.

When adding additional metadata please use the CamelCase version of
[DICOM ontology terms](https://scicrunch.org/scicrunch/interlex/dashboard)
[DICOM ontology terms](https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_d.html)
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that's pretty much the only one where I am not so sure this is the best link for this

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I wonder if https://bioportal.bioontology.org/ontologies/DCM might not be better. @dbkeator Any thoughts?

whenever possible. See also
[recommendations on JSON files](../common-principles.md#keyvalue-files-dictionaries).

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4 changes: 2 additions & 2 deletions src/modality-specific-files/magnetoencephalography.md
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Expand Up @@ -408,10 +408,10 @@ A guide for using macros can be found at
{{ MACROS___make_sidecar_table("meg.MEGCoordsystemFiducialsInformation") }}

For more information on the definition of anatomical landmarks, please visit:
[https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined)
[https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined/)
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For more information on typical coordinate systems for MEG-MRI coregistration:
[https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined),
[https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined/),
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or:
[https://neuroimage.usc.edu/brainstorm/CoordinateSystems](https://neuroimage.usc.edu/brainstorm/CoordinateSystems)

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2 changes: 1 addition & 1 deletion src/modality-specific-files/microscopy.md
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Expand Up @@ -434,7 +434,7 @@ sub-02 mus musculus C57BL/6J RRID:IMSR_JAX:000664
"Description": "name of the strain of the species"
},
"strain_rrid": {
"Description": "research resource identifier (RRID) of the strain (https://scicrunch.org/resources/Organisms/search)"
"Description": "research resource identifier (RRID) of the strain (https://scicrunch.org/resources/data/source/nlx_154697-1/search)"
}
}
```
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2 changes: 1 addition & 1 deletion src/schema/objects/columns.yaml
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Expand Up @@ -568,7 +568,7 @@ strain_rrid:
display_name: Strain RRID
description: |
For species different from `homo sapiens`, research resource identifier
([RRID](https://scicrunch.org/resources/Organisms/search))
([RRID](https://scicrunch.org/resources/data/source/nlx_154697-1/search))
of the strain of the species, for example: `RRID:IMSR_JAX:000664`.
type: string
format: rrid
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16 changes: 9 additions & 7 deletions src/schema/objects/extensions.yaml
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Expand Up @@ -100,9 +100,9 @@ fdt:
value: .fdt
display_name: EEGLAB FDT
description: |
An [EEGLAB](https://sccn.ucsd.edu/eeglab) file.
An [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php) file.

The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab).
The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php).
Each recording consists of a `.set` file with an optional `.fdt` file.
fif:
value: .fif
Expand Down Expand Up @@ -175,8 +175,10 @@ OMEZARR:
description: |
An OME-NGFF file.

OME-NGFF is a [Zarr](https://zarr.readthedocs.io)-based format, organizing data arrays in nested directories.
This format was developed by the Open Microscopy Environment to provide data stream access to very large data.
OME-NGFF is a [Zarr](https://zarr.readthedocs.io/en/stable/)-based format,
organizing data arrays in nested directories.
This format was developed by the Open Microscopy Environment
to provide data stream access to very large data.
nii:
value: .nii
display_name: NIfTI
Expand All @@ -191,7 +193,7 @@ nwb:
value: .nwb
display_name: Neurodata Without Borders Format
description: |
A [Neurodata Without Borders](https://nwb-schema.readthedocs.io) file.
A [Neurodata Without Borders](https://nwb-schema.readthedocs.io/en/latest/) file.

Each recording consists of a single `.nwb` file.
OMEBigTiff:
Expand Down Expand Up @@ -233,9 +235,9 @@ set:
value: .set
display_name: EEGLAB SET
description: |
An [EEGLAB](https://sccn.ucsd.edu/eeglab) file.
An [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php) file.

The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab).
The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php).
Each recording consists of a `.set` file with an optional `.fdt` file.
snirf:
value: .snirf
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4 changes: 2 additions & 2 deletions src/schema/objects/files.yaml
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Expand Up @@ -9,8 +9,8 @@ CHANGES:
Version history of the dataset (describing changes, updates and corrections) MAY be provided in
the form of a `CHANGES` text file.
This file MUST follow the
[CPAN Changelog convention](https://metacpan.org/pod/release/HAARG/CPAN-Changes-0.400002/lib/\
CPAN/Changes/Spec.pod).
[CPAN Changelog convention](https://metacpan.org/release/HAARG/CPAN-Changes-0.400002/view\
/lib/CPAN/Changes/Spec.pod).
The `CHANGES` file MUST be either in ASCII or UTF-8 encoding.
CITATION:
display_name: CITATION.cff
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