diff --git a/mkdocs.yml b/mkdocs.yml index be262a8910..8779cf916c 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -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: diff --git a/src/appendices/coordinate-systems.md b/src/appendices/coordinate-systems.md index 5a484e312f..28b50ab9bb 100644 --- a/src/appendices/coordinate-systems.md +++ b/src/appendices/coordinate-systems.md @@ -195,25 +195,25 @@ Unless specified explicitly in the sidecar file in the ### Standard template identifiers -| **Coordinate System** | **Description** | **Used by** | **Reference** | -| ---------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------ | ---------------------------------------------------------------------------------------------------------------------------------- | -| 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. | SPM12 | [https://brain-development.org/](https://brain-development.org/) | -| fsaverage | 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\[3\|4\|5\|6\|sym\]). | Freesurfer | | -| fsaverageSym | 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 `fsaverageSym` atlas also defines a symmetric surface reference system (formerly described as `fsaveragesym`). | Freesurfer | | -| 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. | Freesurfer | | -| MNIColin27 | Average of 27 T1 scans of a single subject | SPM96 | [https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres](https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres) | -| MNI152Lin | Also known as ICBM (version with linear coregistration) | SPM99 to SPM8 | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin](https://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 flavors each in symmetric or asymmetric version. | DARTEL toolbox in SPM12b | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) | -| MNI152NLin6Sym | Also known as symmetric ICBM 6th generation (non-linear coregistration). | FSL | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](https://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. | HCP-Pipelines | [doi:10.1016/j.neuroimage.2012.01.024](https://doi.org/10.1016/j.neuroimage.2012.01.024) | -| 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. | | [https://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1](https://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://talairach.org/](http://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) | +| **Coordinate System** | **Description** | **Used by** | **Reference** | +| ---------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------- | +| 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. | SPM12 | [https://brain-development.org/](https://brain-development.org/) | +| fsaverage | 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\[3\|4\|5\|6\|sym\]). | Freesurfer | | +| fsaverageSym | 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 `fsaverageSym` atlas also defines a symmetric surface reference system (formerly described as `fsaveragesym`). | Freesurfer | | +| 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. | Freesurfer | | +| MNIColin27 | Average of 27 T1 scans of a single subject | SPM96 | [https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres](https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres) | +| MNI152Lin | Also known as ICBM (version with linear coregistration) | SPM99 to SPM8 | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin](https://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 flavors each in symmetric or asymmetric version. | DARTEL toolbox in SPM12b | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) | +| MNI152NLin6Sym | Also known as symmetric ICBM 6th generation (non-linear coregistration). | FSL | [https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](https://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. | HCP-Pipelines | [doi:10.1016/j.neuroimage.2012.01.024](https://doi.org/10.1016/j.neuroimage.2012.01.024) | +| 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. | | [https://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1](https://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1) | +| OASIS30AntsOASISAnts | | | [https://figshare.com/articles/dataset/ANTs_ANTsR_Brain_Templates/915436](https://figshare.com/articles/dataset/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://talairach.org/](http://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. diff --git a/src/appendices/hed.md b/src/appendices/hed.md index abbe092d32..866f795cf1 100644 --- a/src/appendices/hed.md +++ b/src/appendices/hed.md @@ -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`) diff --git a/src/appendices/meg-file-formats.md b/src/appendices/meg-file-formats.md index e16c86fe20..6b3730a543 100644 --- a/src/appendices/meg-file-formats.md +++ b/src/appendices/meg-file-formats.md @@ -57,8 +57,8 @@ 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) +To learn more about CTF’s data organization +on the relevant [FieldTrip webpage](https://www.fieldtriptoolbox.org/getting_started/ctf/) ## Neuromag/Elekta/MEGIN @@ -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 @@ -301,8 +301,8 @@ 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) +More about the 4D neuroimaging/BTi data organization +on the relevant [FieldTrip webpage](https://www.fieldtriptoolbox.org/getting_started/bti/) ## KIT/Yokogawa/Ricoh @@ -355,8 +355,8 @@ While the acquisition entity can take any value, it is RECOMMENDED that if the two marker measurements occur before and after the raw data acquisition, `pre` and `post` are used to differentiate the two situations. -More about the KIT/Yokogawa/Ricoh data organization at: -[https://www.fieldtriptoolbox.org/getting_started/yokogawa](https://www.fieldtriptoolbox.org/getting_started/yokogawa/) +More about the KIT/Yokogawa/Ricoh data organization +on the relevant [FieldTrip webpage](https://www.fieldtriptoolbox.org/getting_started/yokogawa/) ## KRISS diff --git a/src/introduction.md b/src/introduction.md index 4e54d79157..7ca079302a 100644 --- a/src/introduction.md +++ b/src/introduction.md @@ -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) diff --git a/src/modality-specific-files/electroencephalography.md b/src/modality-specific-files/electroencephalography.md index 781993e1bc..46ffce2921 100644 --- a/src/modality-specific-files/electroencephalography.md +++ b/src/modality-specific-files/electroencephalography.md @@ -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 @@ -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) + [How are the Left and Right Pre-Auricular (LPA and RPA) points defined? - FieldTrip Toolbox](https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined/) - 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) + [How are the different head and MRI coordinate systems defined? - FieldTrip Toolbox](https://www.fieldtriptoolbox.org/faq/coordsys/) General fields: diff --git a/src/modality-specific-files/intracranial-electroencephalography.md b/src/modality-specific-files/intracranial-electroencephalography.md index 56d047a6b6..339609699d 100644 --- a/src/modality-specific-files/intracranial-electroencephalography.md +++ b/src/modality-specific-files/intracranial-electroencephalography.md @@ -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 diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md index 63effbfa1d..b8a1bcca0d 100644 --- a/src/modality-specific-files/magnetic-resonance-imaging-data.md +++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md @@ -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) whenever possible. See also [recommendations on JSON files](../common-principles.md#keyvalue-files-dictionaries). diff --git a/src/modality-specific-files/magnetoencephalography.md b/src/modality-specific-files/magnetoencephalography.md index c064b64209..c5aff67dcb 100644 --- a/src/modality-specific-files/magnetoencephalography.md +++ b/src/modality-specific-files/magnetoencephalography.md @@ -408,12 +408,12 @@ 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) + [How are the Left and Right Pre-Auricular (LPA and RPA) points defined? - FieldTrip Toolbox](https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined/) 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), + [How are the different head and MRI coordinate systems defined? - FieldTrip Toolbox](https://www.fieldtriptoolbox.org/faq/coordsys/) or: -[https://neuroimage.usc.edu/brainstorm/CoordinateSystems](https://neuroimage.usc.edu/brainstorm/CoordinateSystems) +[Coordinate Systems - Brainstorm toolbox](https://neuroimage.usc.edu/brainstorm/CoordinateSystems) ## Landmark photos (`*_photo.`) diff --git a/src/modality-specific-files/microscopy.md b/src/modality-specific-files/microscopy.md index f70e521321..f66dca928f 100644 --- a/src/modality-specific-files/microscopy.md +++ b/src/modality-specific-files/microscopy.md @@ -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)" } } ``` diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 90f6c56091..b52da751fe 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -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 diff --git a/src/schema/objects/extensions.yaml b/src/schema/objects/extensions.yaml index 1a0dc4d299..96056e497d 100644 --- a/src/schema/objects/extensions.yaml +++ b/src/schema/objects/extensions.yaml @@ -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 @@ -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 @@ -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: @@ -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 diff --git a/src/schema/objects/files.yaml b/src/schema/objects/files.yaml index 8adb534619..ce3bfb29a2 100644 --- a/src/schema/objects/files.yaml +++ b/src/schema/objects/files.yaml @@ -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