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[ENH] BEP022 - Magnetic Resonance Spectroscopy #1377

Merged
merged 111 commits into from
Aug 26, 2024
Merged

[ENH] BEP022 - Magnetic Resonance Spectroscopy #1377

merged 111 commits into from
Aug 26, 2024

Commits on Oct 25, 2022

  1. First commit of bep022 into BIDS 

    Adding and changing files to introduce MRS to the BIDS specification.
    @markmikkelsen
    markmikkelsen committed Oct 25, 2022
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Commits on Oct 28, 2022

  1. More additions for bep022 

    - Added future publication ref in 01-introduction.md
- Added table of MRS sequences
- Starting to add new details for the MRS JSON sidecar
- Added MRS-MRI correspondence in Appendix
- Added volume as a new entity
- Changed order of MRS suffixes in src/schema/rulesfiles/raw/mrs.yaml
    @markmikkelsen
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Commits on Dec 7, 2022

  1. Further updates for bep022

    @markmikkelsen
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  2. Further updates

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Commits on Dec 8, 2022

  1. Adding more metadata to MRS-specific fields

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  2. Finalizing additions for bep022

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Commits on Dec 9, 2022

  1. Minor update

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  2. Spelling correction

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Commits on Jan 5, 2023

  1. Update contributors.md

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Commits on Jan 6, 2023

  1. Some minor edits

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  2. Merge remote-tracking branch 'upstream/master' into bep022

    @effigies
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Commits on Jan 10, 2023

  1. Some minor changes and fixes to automatic checks.

    @markmikkelsen
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  2. Merge branch 'bep022' of https://github.com/markmikkelsen/bids-specif… 

    …ication into bep022
    @markmikkelsen
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  3. Table style correction

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Commits on Jan 11, 2023

  1. Further corrections to fix check failures

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Commits on Jan 12, 2023

  1. Further corrections to fix check failures (2)

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  2. DOC: Remove 02- from common principles URL, drop DEPRECATED option.

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  3. Merge remote-tracking branch 'upstream/master' into bep022

    @effigies
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  4. FIX: Remove 04- and 01- from MRI links

    @effigies
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  5. FIX: Macro formatting

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  6. FIX: More numeric prefixes

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Commits on Jan 27, 2023

  1. Remove DEPRECATED functionalities

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  2. Change URL to NIfTI-MRS paper

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  3. Update src/schema/rules/sidecars/mrs.yaml 

    Change `NumberOfTransients` to be recommended for SVS and unloc data only; optional otherwise.

Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
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  4. Update mrs.yaml

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Commits on Feb 7, 2023

  1. Update README.md; minor cosmetic change

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Commits on Aug 24, 2023

  1. Merge branch 'master' into bep022

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  2. Update src/schema/objects/metadata.yaml

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Commits on Sep 7, 2023

  1. Merge branch 'master' into bep022

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  2. Merge pull request #1 from bids-standard/bep022 

    Bep022
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Commits on Nov 27, 2023

  1. Merge branch 'master' into bep022

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  2. STY: Cleanup apparent merge artifacts

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  3. Merge branch 'bids-standard:bep022' into bep022

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Commits on Dec 19, 2023

  1. Update src/modality-specific-files/magnetic-resonance-spectroscopy.md 

    Co-authored-by: Julia Guiomar Niso Galán <guiomar.niso@ctb.upm.es>
    @markmikkelsen @guiomar
    markmikkelsen and guiomar committed Dec 19, 2023
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  2. Update src/modality-specific-files/magnetic-resonance-spectroscopy.md 

    Co-authored-by: Julia Guiomar Niso Galán <guiomar.niso@ctb.upm.es>
    @markmikkelsen @guiomar
    markmikkelsen and guiomar committed Dec 19, 2023
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  3. Update src/modality-specific-files/magnetic-resonance-spectroscopy.md 

    Co-authored-by: Julia Guiomar Niso Galán <guiomar.niso@ctb.upm.es>
    @markmikkelsen @guiomar
    markmikkelsen and guiomar committed Dec 19, 2023
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  4. Merge branch 'bep022' of https://github.com/markmikkelsen/bids-specif… 

    …ication into bep022
    @markmikkelsen
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Commits on Dec 20, 2023

  1. Update src/modality-specific-files/magnetic-resonance-spectroscopy.md 

    Co-authored-by: Julia Guiomar Niso Galán <guiomar.niso@ctb.upm.es>
    @markmikkelsen @guiomar
    markmikkelsen and guiomar committed Dec 20, 2023
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  2. Update src/modality-specific-files/magnetic-resonance-spectroscopy.md 

    Co-authored-by: Julia Guiomar Niso Galán <guiomar.niso@ctb.upm.es>
    @markmikkelsen @guiomar
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  3. Merge branch 'bids-standard:bep022' into bep022

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  4. Update src/modality-specific-files/magnetic-resonance-spectroscopy.md 

    Co-authored-by: Julia Guiomar Niso Galán <guiomar.niso@ctb.upm.es>
    @markmikkelsen @guiomar
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Commits on Dec 21, 2023

  1. Merge branch 'bids-standard:bep022' into bep022

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Commits on Feb 28, 2024

  1. Merge branch 'master' into bep022

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  2. Merge branch 'bids-standard:bep022' into bep022

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Commits on Feb 29, 2024

  1. Merge branch 'master' into bep022

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  2. Merge branch 'bep022' of https://github.com/markmikkelsen/bids-specif… 

    …ication into bep022
    @markmikkelsen
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  3. Update mrs.yaml

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  4. Update entities.yaml

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  5. Further updates

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Commits on Mar 1, 2024

  1. Update the MRAcquisitionType schema

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  2. Update contributors.md

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  3. Revert "Update contributors.md" 

    This reverts commit f9b1eef.
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  4. Revert "Update contributors.md" 

    This reverts commit f9b1eef.
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  5. Merge branch 'bids-standard:bep022' into bep022

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  6. Add a section about MRS-MRI correspondence

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Commits on Mar 21, 2024

  1. Merge branch 'master' into bep022

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  2. Update magnetic-resonance-spectroscopy.md 

    Add Mkdocs admonition to example datasets paragraph
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Commits on Mar 28, 2024

  1. Change tissue description requirement levels in MRS to optional

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  2. Update MRS-MRI correspondence

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  3. Change suffix ref to mrsref

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  4. Update magnetic-resonance-spectroscopy.md 

    Adding metabolite-cycled spectroscopy to MRS sequences
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  5. Update mrs.yaml

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Commits on Apr 8, 2024

  1. Merge branch 'master' into bep022

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Commits on Apr 9, 2024

  1. Update magnetic-resonance-spectroscopy.md 

    - Cosmetic edits
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  2. Merge pull request #1766 from markmikkelsen/bep022 

    Update magnetic-resonance-spectroscopy.md
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Commits on Apr 11, 2024

  1. Merge branch 'master' into bep022

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Commits on Apr 13, 2024

  1. Cleaning up language

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  2. Merge pull request #1776 from markmikkelsen/bep022 

    Cleaning up language
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  3. Update mrs.yaml 

    - Reorder MRS fields to coincide with (now) shared MRI fields
    @markmikkelsen
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  4. Merge branch 'bep022' into bep022

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  5. Merge pull request #1777 from markmikkelsen/bep022 

    Update mrs.yaml
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Commits on Apr 16, 2024

  1. Merge branch 'master' into bep022

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Commits on Apr 20, 2024

  1. Apply suggestions from code review 

    Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
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Commits on Apr 21, 2024

  1. Merge branch 'master' into bep022

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Commits on Apr 22, 2024

  1. Update magnetic-resonance-spectroscopy.md 

    - Add NIfTI paper DOI
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  2. Update magnetic-resonance-spectroscopy.md 

    - Fix table at lines 69-74
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  3. Merge branch 'master' into bep022

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Commits on Apr 24, 2024

  1. Merge branch 'master' into bep022

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Commits on Apr 25, 2024

  1. Merge branch 'master' into bep022

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Commits on Apr 26, 2024

  1. Merge branch 'master' into bep022

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Commits on Apr 27, 2024

  1. Merge branch 'master' into bep022

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Commits on Apr 30, 2024

  1. Merge branch 'master' into bep022

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Commits on May 1, 2024

  1. Update mrs.yaml 

    - Change 'EditTarget', 'EditPulse', and 'EditCondition' to 'optional'
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Commits on May 2, 2024

  1. Update src/schema/objects/metadata.yaml 

    Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
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  2. Update magnetic-resonance-spectroscopy.md 

    - Change "MRS-specific" to "MRS-relevant"
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  3. Set OuterVolumeSuppression as optional

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  4. Update fields for MRS

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  5. Update metadata.yaml 

    - Minor grammar change
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Commits on May 8, 2024

  1. Some further changes 

    - Reordered recommended MRS-relevant fields
- Some rearranging of src/schema/rules/sidecars/mrs.yaml
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Commits on May 16, 2024

  1. Merge branch 'master' into bep022

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Commits on May 21, 2024

  1. Merge branch 'master' into bep022

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Commits on May 28, 2024

  1. Merge branch 'master' into bep022

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Commits on May 29, 2024

  1. Update metadata.yaml 

    - Spelling correction
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  2. Update src/schema/objects/metadata.yaml 

    Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
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  3. Update src/schema/objects/metadata.yaml 

    Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
    @markmikkelsen @effigies
    markmikkelsen and effigies committed May 29, 2024
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  4. Merge branch 'bids-standard:bep022' into bep022

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    markmikkelsen committed May 29, 2024
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Commits on May 31, 2024

  1. Merge branch 'master' into bep022

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  2. SCHEMA: Add nifti_header.mrs to context

    @effigies
    effigies committed May 31, 2024
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  3. SCHEMA: Add check for consistency between MRS header and sidecar

    @effigies
    effigies committed May 31, 2024
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  4. Split conditional matrices in schema, combine in doc 

    This implements the following agreed upon suggestions:

* Set InversionTime to recommended if `inv` entity is present.
  (`entities.inversion`)
* Move to RepetitionTime and VolumeTiming, rather than RepetitionTime
  as an array in the variable-timing case.
* ReferenceSignal should be uniformly recommended.
    @effigies
    effigies committed May 31, 2024
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  5. Make BodyPart(Details) required if voi entity is present

    @effigies
    effigies committed May 31, 2024
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  6. feat(checks): Add check to ensure MatrixSize and nifti_header.dim are… 

    … consistent
    @effigies
    effigies committed May 31, 2024
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  7. fix(checks): Use non-trivial expressions for selectors

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    effigies committed May 31, 2024
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Commits on Jun 1, 2024

  1. Uncombine required/recommended/optional fields

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    effigies committed Jun 1, 2024
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  2. Merge pull request #1830 from effigies/schema/mrs_header 

    [SCHEMA] MRS schema updates
    @markmikkelsen
    markmikkelsen committed Jun 1, 2024
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  3. Merge branch 'master' into bep022

    @markmikkelsen
    markmikkelsen committed Jun 1, 2024
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Commits on Jul 24, 2024

  1. Merge branch 'master' into bep022

    @effigies
    effigies committed Jul 24, 2024
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Commits on Jul 25, 2024

  1. Update src/schema/rules/sidecars/func.yaml 

    Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu>
    @markmikkelsen @tsalo
    markmikkelsen and tsalo committed Jul 25, 2024
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  2. FIX: Add MRS events files, restrict sidecar metadata checks to data f… 

    …iles (#1875)

* FIX: Add MRS events files, restrict sidecar metadata checks to data files

* FIX: Do not limit suffixes for filename template
    @effigies
    effigies committed Jul 25, 2024
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Commits on Aug 7, 2024

  1. Merge branch 'master' into bep022

    @effigies
    effigies committed Aug 7, 2024
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Commits on Aug 22, 2024

  1. Merge branch 'master' into bep022

    @effigies
    effigies committed Aug 22, 2024
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