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@Remi-Gau
Remi-Gau committed Sep 25, 2023
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2 changes: 1 addition & 1 deletion src/appendices/coordinate-systems.md
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Expand Up @@ -212,7 +212,7 @@ Unless specified explicitly in the sidecar file in the
| 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/) |
| Talairach | Piecewise linear scaling of the brain is implemented as described in TT88. | | [https://talairach.org/](https://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
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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:
[http://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined](http://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)

For more information on typical coordinate systems for MEG-MRI coregistration:
[http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined](http://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),
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 @@ -47,7 +47,7 @@ tiled format, or vice-versa.

Microscopy raw data MUST be stored in one of the following formats:

- [Portable Network Graphics](http://www.libpng.org/pub/png/) (`.png`)
- [Portable Network Graphics](https://www.libpng.org/pub/png/) (`.png`)

- [Tag Image File Format](https://en.wikipedia.org/wiki/TIFF) (`.tif`)

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2 changes: 1 addition & 1 deletion src/schema/objects/extensions.yaml
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Expand Up @@ -208,7 +208,7 @@ png:
value: .png
display_name: Portable Network Graphics
description: |
A [Portable Network Graphics](http://www.libpng.org/pub/png/) file.
A [Portable Network Graphics](https://www.libpng.org/pub/png/) file.
pos:
value: .pos
display_name: Head Point Position
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10 changes: 5 additions & 5 deletions src/schema/objects/metadata.yaml
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Expand Up @@ -385,7 +385,7 @@ CellType:
description: |
Describes the type of cell analyzed.
Values SHOULD come from the
[cell ontology](http://obofoundry.org/ontology/cl.html).
[cell ontology](https://obofoundry.org/ontology/cl.html).
type: string
ChunkTransformationMatrix:
name: ChunkTransformationMatrix
Expand Down Expand Up @@ -453,7 +453,7 @@ CogPOID:
display_name: Cognitive Paradigm Ontology ID
description: |
[URI](SPEC_ROOT/common-principles.md#uniform-resource-indicator)
of the corresponding [CogPO](http://www.cogpo.org/) term.
of the corresponding [CogPO](https://www.cogpo.org/) term.
type: string
format: uri
CoilCombinationMethod:
Expand Down Expand Up @@ -2638,10 +2638,10 @@ RepetitionTime:
and the beginning of acquisition of the volume following it (TR).
When used in the context of functional acquisitions this parameter best
corresponds to
[DICOM Tag 0020, 0110](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0020,0110)):
[DICOM Tag 0020, 0110](https://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0020,0110)):
the "time delta between images in a
dynamic of functional set of images" but may also be found in
[DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)):
[DICOM Tag 0018, 0080](https://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)):
"the period of time in msec between the beginning
of a pulse sequence and the beginning of the succeeding
(essentially identical) pulse sequence".
Expand All @@ -2658,7 +2658,7 @@ RepetitionTimeExcitation:
display_name: Repetition Time Excitation
description: |
The interval, in seconds, between two successive excitations.
[DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080))
[DICOM Tag 0018, 0080](https://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080))
best refers to this parameter.
This field may be used together with the `"RepetitionTimePreparation"` for
certain use cases, such as
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