From f6bcb0a147effefc7bdc72622d885fbd53ee6310 Mon Sep 17 00:00:00 2001 From: Jan Valosek <39456460+valosekj@users.noreply.github.com> Date: Mon, 25 Sep 2023 16:07:12 +0200 Subject: [PATCH 1/2] [ENH] Add "chunk" entity to MRI images (#1586) * Add 'chunk' entity to MRI datatype * Update wording of chunk entitty Co-authored-by: Chris Markiewicz * Remove MRI paragraph from ChunkTransformationMatrix description * Add chunk entity for fieldmaps * Add chunk entity for multiecho --------- Co-authored-by: Chris Markiewicz Co-authored-by: Remi Gau --- src/schema/objects/entities.yaml | 9 ++++++--- src/schema/rules/files/raw/anat.yaml | 9 +++++++++ src/schema/rules/files/raw/dwi.yaml | 2 ++ src/schema/rules/files/raw/fmap.yaml | 7 +++++++ src/schema/rules/files/raw/func.yaml | 2 ++ 5 files changed, 26 insertions(+), 3 deletions(-) diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml index bc0af52289..6facc34c0d 100644 --- a/src/schema/objects/entities.yaml +++ b/src/schema/objects/entities.yaml @@ -41,9 +41,12 @@ chunk: name: chunk display_name: Chunk description: | - The `chunk-` key/value pair is used to distinguish between different regions, - 2D images or 3D volumes files, - of the same physical sample with different fields of view acquired in the same imaging experiment. + The `chunk-` key/value pair is used to distinguish between images of + the same physical sample with different fields of view acquired in the same + imaging experiment. + This entity applies to collections of 2D images, 3D volumes or 4D volume series + (for example, diffusion weighted images), and may be used to indicate different + anatomical structures or regions of the same structure. type: string format: index density: diff --git a/src/schema/rules/files/raw/anat.yaml b/src/schema/rules/files/raw/anat.yaml index 3e026107f4..7a8a3234e6 100644 --- a/src/schema/rules/files/raw/anat.yaml +++ b/src/schema/rules/files/raw/anat.yaml @@ -29,6 +29,7 @@ nonparametric: run: optional echo: optional part: optional + chunk: optional parametric: suffixes: @@ -62,6 +63,7 @@ parametric: ceagent: optional reconstruction: optional run: optional + chunk: optional defacemask: suffixes: @@ -81,6 +83,7 @@ defacemask: reconstruction: optional run: optional modality: optional + chunk: optional multiecho: suffixes: @@ -102,6 +105,7 @@ multiecho: run: optional echo: required part: optional + chunk: optional multiflip: suffixes: @@ -123,6 +127,7 @@ multiflip: echo: optional flip: required part: optional + chunk: optional multiinversion: suffixes: @@ -143,6 +148,7 @@ multiinversion: run: optional inversion: required part: optional + chunk: optional mp2rage: suffixes: @@ -165,6 +171,7 @@ mp2rage: flip: optional inversion: required part: optional + chunk: optional vfamt: suffixes: @@ -188,6 +195,7 @@ vfamt: flip: required mtransfer: required part: optional + chunk: optional mtr: suffixes: @@ -208,3 +216,4 @@ mtr: run: optional mtransfer: required part: optional + chunk: optional diff --git a/src/schema/rules/files/raw/dwi.yaml b/src/schema/rules/files/raw/dwi.yaml index 98840ef6a1..22b224b023 100644 --- a/src/schema/rules/files/raw/dwi.yaml +++ b/src/schema/rules/files/raw/dwi.yaml @@ -18,6 +18,7 @@ dwi: direction: optional run: optional part: optional + chunk: optional sbref: suffixes: @@ -36,3 +37,4 @@ sbref: direction: optional run: optional part: optional + chunk: optional diff --git a/src/schema/rules/files/raw/fmap.yaml b/src/schema/rules/files/raw/fmap.yaml index 8f5e66a508..94b03f7f6f 100644 --- a/src/schema/rules/files/raw/fmap.yaml +++ b/src/schema/rules/files/raw/fmap.yaml @@ -19,6 +19,7 @@ fieldmaps: session: optional acquisition: optional run: optional + chunk: optional pepolar: suffixes: @@ -37,6 +38,7 @@ pepolar: ceagent: optional direction: required run: optional + chunk: optional TB1DAM: suffixes: @@ -57,6 +59,7 @@ TB1DAM: flip: required inversion: optional part: optional + chunk: optional TB1EPI: suffixes: @@ -78,6 +81,7 @@ TB1EPI: flip: required inversion: optional part: optional + chunk: optional RFFieldMaps: suffixes: @@ -102,6 +106,7 @@ RFFieldMaps: flip: optional inversion: optional part: optional + chunk: optional TB1SRGE: suffixes: @@ -123,6 +128,7 @@ TB1SRGE: flip: required inversion: required part: optional + chunk: optional parametric: suffixes: @@ -141,3 +147,4 @@ parametric: ceagent: optional reconstruction: optional run: optional + chunk: optional diff --git a/src/schema/rules/files/raw/func.yaml b/src/schema/rules/files/raw/func.yaml index 589d187444..5e2c42b813 100644 --- a/src/schema/rules/files/raw/func.yaml +++ b/src/schema/rules/files/raw/func.yaml @@ -21,6 +21,7 @@ func: run: optional echo: optional part: optional + chunk: optional phase: suffixes: @@ -41,3 +42,4 @@ phase: direction: optional run: optional echo: optional + chunk: optional From a340ef0c127fbb8a62ea6308a277a0bd70a22ae5 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Tue, 26 Sep 2023 08:11:17 -0400 Subject: [PATCH 2/2] [MAINT] Remove copyright date from footer (#1615) * update date footer * remove date from footer * fix link * fix link * fix links * Update src/appendices/coordinate-systems.md * links * fix links * remark --------- Co-authored-by: Chris Markiewicz --- mkdocs.yml | 2 +- src/appendices/coordinate-systems.md | 2 +- src/appendices/meg-file-formats.md | 2 +- src/appendices/meg-systems.md | 2 +- src/modality-specific-files/magnetoencephalography.md | 6 +++--- src/schema/objects/metadata.yaml | 2 +- src/schema/rules/sidecars/micr.yaml | 2 +- 7 files changed, 9 insertions(+), 9 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index 04c07297ac..be262a8910 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -51,7 +51,7 @@ theme: logo: images/logo.png features: - navigation.sections -copyright: Copyright © 2018-2022, BIDS Contributors - CC BY 4.0 +copyright: Copyright © BIDS Contributors - CC BY 4.0 extra: generator: false social: diff --git a/src/appendices/coordinate-systems.md b/src/appendices/coordinate-systems.md index 157f327d79..5a484e312f 100644 --- a/src/appendices/coordinate-systems.md +++ b/src/appendices/coordinate-systems.md @@ -86,7 +86,7 @@ of restricted keywords for MEG, EEG, or iEEG, please open a new issue on the Note that the short descriptions below may not capture all details. For detailed descriptions of the coordinate systems below, please see the -[FieldTrip webpage](https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined). +[FieldTrip webpage](https://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined/). ### Commonly used anatomical landmarks in MEG, EEG, and iEEG research diff --git a/src/appendices/meg-file-formats.md b/src/appendices/meg-file-formats.md index c6f8649064..e16c86fe20 100644 --- a/src/appendices/meg-file-formats.md +++ b/src/appendices/meg-file-formats.md @@ -356,7 +356,7 @@ 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) +[https://www.fieldtriptoolbox.org/getting_started/yokogawa](https://www.fieldtriptoolbox.org/getting_started/yokogawa/) ## KRISS diff --git a/src/appendices/meg-systems.md b/src/appendices/meg-systems.md index ef5bd613d1..189d0ead31 100644 --- a/src/appendices/meg-systems.md +++ b/src/appendices/meg-systems.md @@ -20,7 +20,7 @@ Restricted keywords for ManufacturersModelName field in the `*_meg.json` file: | CTF-275 | CTF | CTF-275: OMEGA 2000 | | Neuromag-122 | Neuromag/Elekta/Megin | | | ElektaVectorview | Neuromag/Elekta/Megin | 102 magnetometers + 204 planar gradiometers | -| ElektaTRIUX | Neuromag/Elekta/Megin | [https://www.elekta.com/diagnostic-solutions/](https://www.elekta.com/diagnostic-solutions/) | +| ElektaTRIUX | Neuromag/Elekta/Megin | [https://www.elekta.com/products/neurosurgery/](https://www.elekta.com/products/neurosurgery/) | | 4D-Magnes-WH2500 | BTi/4D | | | 4D-Magnes-WH3600 | BTi/4D | | | KIT-157 | KIT/Yokogawa | | diff --git a/src/modality-specific-files/magnetoencephalography.md b/src/modality-specific-files/magnetoencephalography.md index 490662d34a..c064b64209 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: -[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: -[http://neuroimage.usc.edu/brainstorm/CoordinateSystems](http://neuroimage.usc.edu/brainstorm/CoordinateSystems) +[https://neuroimage.usc.edu/brainstorm/CoordinateSystems](https://neuroimage.usc.edu/brainstorm/CoordinateSystems) ## Landmark photos (`*_photo.`) diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index b26e5e78fc..3e7d3e59a6 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -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 diff --git a/src/schema/rules/sidecars/micr.yaml b/src/schema/rules/sidecars/micr.yaml index 0fa46bfcf8..f2f490953f 100644 --- a/src/schema/rules/sidecars/micr.yaml +++ b/src/schema/rules/sidecars/micr.yaml @@ -50,7 +50,7 @@ MicroscopySample: level: recommended description_addendum: | From [DICOM Body Part - Examined](http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) + Examined](https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L) (for example `"BRAIN"`). BodyPartDetails: recommended BodyPartDetailsOntology: optional