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[ENH] BEP 003: Common Derivatives #265

Merged
merged 236 commits into from
Jun 10, 2020
Merged

[ENH] BEP 003: Common Derivatives #265

merged 236 commits into from
Jun 10, 2020

Commits on Dec 16, 2018

  1. Adding derivatives

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  2. adding derivatives to the index

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    chrisgorgo committed Dec 16, 2018
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  3. rename

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  4. rename

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  5. fix index

    @chrisgorgo
    chrisgorgo committed Dec 16, 2018
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  6. fixed links

    @chrisgorgo
    chrisgorgo committed Dec 16, 2018
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  7. fixed links

    @chrisgorgo
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Commits on Dec 31, 2018

  1. template cleanup

    @chrisgorgo
    chrisgorgo committed Dec 31, 2018
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Commits on Jan 3, 2019

  1. Update src/05-derivatives/05-diffusion-derivatives.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @francopestilli @chrisgorgo
    francopestilli and chrisgorgo committed Jan 3, 2019
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  2. Update src/05-derivatives/05-diffusion-derivatives.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @francopestilli @chrisgorgo
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  3. Update src/05-derivatives/05-diffusion-derivatives.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @francopestilli @chrisgorgo
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  4. Update src/05-derivatives/05-diffusion-derivatives.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @francopestilli @chrisgorgo
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  5. Update src/05-derivatives/05-diffusion-derivatives.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @francopestilli @chrisgorgo
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  6. Update src/05-derivatives/05-diffusion-derivatives.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @francopestilli @chrisgorgo
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  7. Update src/05-derivatives/05-diffusion-derivatives.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @francopestilli @chrisgorgo
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  8. Update src/05-derivatives/05-diffusion-derivatives.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @francopestilli @chrisgorgo
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  9. Merge branch 'master' of github.com:bids-standard/bids-specification … 

    …into enh/derivatives
    @chrisgorgo
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  10. syntax fixes

    @chrisgorgo
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  11. remove old extensions

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Commits on Feb 28, 2019

  1. Merge branch 'master' of github.com:bids-standard/bids-specification … 

    …into enh/derivatives
    @chrisgorgo
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  2. Update src/99-appendices/08-coordinate-systems.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @satra @chrisgorgo
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  3. Update src/99-appendices/08-coordinate-systems.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @satra @chrisgorgo
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  4. bring back space

    @chrisgorgo
    chrisgorgo committed Feb 28, 2019
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Commits on Mar 4, 2019

  1. Update src/05-derivatives/01-introduction.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @effigies @chrisgorgo
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  2. Update src/05-derivatives/01-introduction.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @effigies @chrisgorgo
    effigies and chrisgorgo committed Mar 4, 2019
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  3. Update src/05-derivatives/02-common-data-types.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @yarikoptic @chrisgorgo
    yarikoptic and chrisgorgo committed Mar 4, 2019
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  4. Update src/99-appendices/08-coordinate-systems.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @effigies @chrisgorgo
    effigies and chrisgorgo committed Mar 4, 2019
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  5. Update src/05-derivatives/02-common-data-types.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @effigies @chrisgorgo
    effigies and chrisgorgo committed Mar 4, 2019
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  6. Update src/05-derivatives/02-common-data-types.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @effigies @chrisgorgo
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  7. Update src/05-derivatives/03-structural-derivatives.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @effigies @chrisgorgo
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  8. Update src/05-derivatives/03-structural-derivatives.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @effigies @chrisgorgo
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  9. Update src/05-derivatives/03-structural-derivatives.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @effigies @chrisgorgo
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  10. fix formatting

    @chrisgorgo
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  11. Merge branch 'master' of github.com:bids-standard/bids-specification … 

    …into enh/derivatives
    @chrisgorgo
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  12. added a rule concerning pipline_name consistency

    @chrisgorgo
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  13. fix spaces

    @chrisgorgo
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  14. get rid of derivatived

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Commits on Mar 5, 2019

  1. add mention of source data in stanalone derivatives datasets

    @chrisgorgo
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  2. fix label T1w example

    @chrisgorgo
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  3. fix missing bracket

    @chrisgorgo
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  4. add missing 'w' in T2w

    @chrisgorgo
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  5. Limit number of allowed suffixes for scalar derivatives

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  6. Update src/99-appendices/08-coordinate-systems.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @effigies @chrisgorgo
    effigies and chrisgorgo committed Mar 5, 2019
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  7. adding CODEOWNERS

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  8. Merge branch 'enh/derivatives' of github.com:chrisfilo/bids-specifica… 

    …tion into enh/derivatives
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  9. adding missing end line

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  10. fix syntax

    @chrisgorgo
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  11. removing group

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Commits on Mar 6, 2019

  1. [ENC] getting rid of type- key 

    I don't know where the type key came from. 
I also tried to remove the reference to a space table in the introduction that has moved (is it in the appendix?)

(I'll post this an issue)
So currently we have. _dseg.tsv suffix for color lookup tables. A label-<label> key value pair for specifying the label in _probseg.nii.gz files. And files with multiple mask (i.e. atlases having a _dseg.nii.gz) extension. And and atlas-<label> key value pair that appears in fmri..

1. is it ok for _dseg.nii.gz and _dseg.tsc to have the same suffix? or are suffixes supposed to associate with a specific file type.
2. technically the _dparc.dlabel.nii could be _dseg.dlabel.nii because they have similar concepts (just cifti vs nifti).
3.
    @edickie
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  2. Merge pull request #3 from edickie/patch-1 

    [ENC] getting rid of type- key
    @chrisgorgo
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  3. bringing back space

    @edickie
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  4. clarify allowed values for 'space'

    @chrisgorgo
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  5. adding volumetric template used in in HCP

    @chrisgorgo
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  6. Merge pull request #4 from edickie/patch-2 

    bringing back space
    @chrisgorgo
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  7. added HCP spaces and introduced hybrid spaces

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  8. shorten labels, add links

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  9. Various proposed changes to diffusion derivatives

    @Lestropie
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  10. Derivatives: Diffusion: Tractography: Split "Parameters" dictionary

    @Lestropie
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  11. FIX: Link subsections in functional derivatives

    @effigies
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  12. Merge pull request #7 from effigies/fix/subsection_links 

    FIX: Link subsections in functional derivatives
    @chrisgorgo
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  13. MNIfsLR32k + clarifications

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  14. small fixes

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  15. Merge branch 'enh/derivatives' of github.com:chrisfilo/bids-specifica… 

    …tion into enh/derivatives
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  16. remove transforms since they are not part of this PR

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  17. remove transforms since they are not part of this PR

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Commits on Mar 7, 2019

  1. Merge branch 'enh/derivatives' into enh/derivatives

    @Lestropie
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  2. ENH: Rename regressors.tsv to timeseries.tsv 

    Add sampling information to clarify interpretation and bring closer
into line with _physio.tsv/_stim.tsv.
    @effigies
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  3. Typo

    @effigies
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  4. ENH: Rework metadata description

    @effigies
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  5. FIX: Subsection name, link

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  6. RF: Remove "regressor" term

    @effigies
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  7. adding myself to contributers

    @edickie
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  8. STY: Slightly less repetitive wording

    @effigies
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  9. Merge pull request #2 from effigies/enh/derivatives 

    ENH: Rename regressors.tsv to timeseries.tsv
    @chrisgorgo
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  10. Merge pull request #8 from edickie/patch-1 

    adding myself to contributors
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  11. HCPMNI

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  12. Merge pull request #5 from chrisfilo/enh/cifti_spaces 

    [ENH] Adding hybrid spaces for CIFTI use
    @chrisgorgo
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  13. fix syntax

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Commits on Mar 8, 2019

  1. fix syntax (for realz now)

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  2. adding very inflated surfaces

    @edickie
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  3. Merge pull request #10 from edickie/patch-3 

    adding very inflated surfaces
    @chrisgorgo
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  4. Update src/05-derivatives/05-diffusion-derivatives.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @oesteban @chrisgorgo
    oesteban and chrisgorgo committed Mar 8, 2019
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Commits on Mar 15, 2019

  1. [INFRA] Adding instructions for naming PRs

    @chrisgorgo
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  2. REF: initial rewriting of coordinate system keys

    @satra
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  3. Update src/05-derivatives/01-introduction.md 

    Co-Authored-By: satra <satrajit.ghosh@gmail.com>
    @chrisgorgo @satra
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Commits on Mar 16, 2019

  1. Further widespread changes to diffusion derivatives 

    Following on from ea2bc96.
- Fix grammattical error in description of DWI JSON.
- Modify description of recommended NODDI model output.
- For "fwDTI" model, separate tensor coefficients and free water fraction data into two separate NIfTI images.
- For DTI model, include iterative weighted least squares as an option, and separate RESTORE (outlier rejection) as being a separate parameter rather than a method of fitting.
- For CSD model, offer two mechanisms for specifying the response function; also remove MRtrix 0.2 SH basis, and remove "none" from NonNegativityConstraint (as without a non-negativity constraint, it would not be CSD).
- Provide additional examples for DWI model outputs.
- Remove NODDI parameters from "model-derived maps", as these are re-classified as fundamental model output parameters.
- Remove DECFA from "model-derived maps", and instead define "directionally-encoded colour maps" as a different form of model-derived map, since any scalar map can be augmented with DEC.
- Add "Count" as a compulsory parameter for tractography output.
- For tractography output, provide three distinct dictionaries within the JSON: "Constraints" (ROIs and anatomical tissue constraints), "Parameters" (for parameters specific to the streamlines tractography algorithm), and "Seeding" (since determining streamline seeds is in fact independent of the particular tractography algorithm and parameters). Field "TerminationCriterion" was removed in this process as it is common for there to be more than one mechanism by which streamlines are terminated. Possibilities for streamline seeding have been more broadly generalised as part of this process.
    @Lestropie
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  2. Resolve build issues in diffusion derivatives

    @Lestropie
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  3. Further resolution of build issues in diffusion derivatives 

    Follows from �18dc84fc.
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  4. Merge pull request #11 from satra/enh/coordinates 

    REF: initial rewriting of coordinate system keys
    @chrisgorgo
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  5. fixes

    @chrisgorgo
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  6. [ENH] CoordinateSystem clarifications and examples

    @chrisgorgo
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  7. [ENH] CoordinateSystem clarifications and examples

    @chrisgorgo
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Commits on Mar 17, 2019

  1. address Satra's comments

    @chrisgorgo
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  2. address Satra's comments

    @chrisgorgo
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Commits on Mar 20, 2019

  1. Merge branch 'master' of github.com:bids-standard/bids-specification … 

    …into enh/space_examples
    @chrisgorgo
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  2. Merge branch 'master' of github.com:bids-standard/bids-specification

    @chrisgorgo
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  3. Merge branch 'master' into enh/derivatives

    @chrisgorgo
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  4. fix a link typo

    @chrisgorgo
    chrisgorgo committed Mar 20, 2019
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  5. removal of the Definition section in Coordinate Spaces appendix

    @chrisgorgo
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  6. Update src/99-appendices/08-coordinate-systems.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @effigies @chrisgorgo
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  7. Update src/99-appendices/08-coordinate-systems.md 

    Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>
    @effigies @chrisgorgo
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  8. Merge branch 'enh/derivatives' into enh/space_examples

    @chrisgorgo
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  9. Merge branch 'enh/space_examples' of github.com:chrisfilo/bids-specif… 

    …ication into enh/space_examples
    @chrisgorgo
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  10. fixes

    @chrisgorgo
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Commits on Mar 21, 2019

  1. adding desc to structural derivatives

    @chrisgorgo
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  2. Merge branch 'enh/derivatives' into enh/space_examples

    @chrisgorgo
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Commits on Mar 22, 2019

  1. anat->native + cleanup

    @chrisgorgo
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  2. cleaning leftover anat's

    @chrisgorgo
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  3. fix syntax

    @chrisgorgo
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  4. clarify links between raw and derived datasets

    @chrisgorgo
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  5. fixes

    @chrisgorgo
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Commits on Mar 24, 2019

  1. native -> individual

    @chrisgorgo
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  2. bringing back custom space

    @chrisgorgo
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  3. add volspace for meshes

    @chrisgorgo
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  4. fixes

    @chrisgorgo
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Commits on Mar 30, 2019

  1. ReferenceMap -> SpatialReference

    @chrisgorgo
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  2. Merge pull request #12 from chrisfilo/enh/space_examples 

    [ENH] replacing `CoordinateSystem` replacement with `space` + examples
    @chrisgorgo
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Commits on Apr 14, 2019

  1. Merge branch 'master' of github.com:bids-standard/bids-specification … 

    …into enh/derivatives
    Chris Gorgolewski committed Apr 14, 2019
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  2. Merge pull request #109 from chrisgorgo/enh/derivatives 

    [ENH] Derived (processed) MR data
    @chrisgorgo
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Commits on Apr 16, 2019

  1. Merge branch 'master' into derivatives

    @effigies
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Commits on Apr 24, 2019

  1. Diffusion derivatives: Further fixes for #205 

    - Minor spelling & grammar fixes.
- In "scalar maps" section, expand out the different parameters to be derived from the ball-and-stick(s) model.
- Provide more accurate link to MRtrix3 tracks file format.
    @Lestropie
    Lestropie committed Apr 24, 2019
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  2. Diffusion derivatives: Formatting 

    - Fix use of superscripts in "Scalar maps" table.
- For "Units" field in tractography JSON file, list possible values in the same format as that used elsewhere in the document.
    @Lestropie
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  3. Diffusion derivatives: Further fix of superscript usage 

    Follows 1d0613e.
    @Lestropie
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  4. Diffusion derivatives: Fix error in DKI & WMTI model descriptions

    @Lestropie
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  5. Diffusion derivatives: Use subscripts in model descriptions

    @Lestropie
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Commits on Apr 30, 2019

  1. DOC: really minor typo

    @yarikoptic
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Commits on May 5, 2019

  1. Merge pull request #205 from Lestropie/enh/derivatives 

    [ENH] Various proposed changes to diffusion derivatives
    @francopestilli
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Commits on May 9, 2019

  1. ENH: use <label> for _desc- - not some <value> + clarify <value>

    @yarikoptic
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  2. Merge pull request #224 from yarikoptic/enh-desc-label 

    [FIX] use <label> for _desc- - not some <value> + clarify <value>
    @effigies
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Commits on May 16, 2019

  1. Merge remote-tracking branch 'upstream/master' into derivatives

    @effigies
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Commits on May 17, 2019

  1. Merge remote-tracking branch 'upstream/master' into derivatives

    @effigies
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Commits on May 28, 2019

  1. FIX: Apply suggestions from @sappelhoff review

    @effigies
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  2. FIX: Code block with indentations

    @effigies
    effigies committed May 28, 2019
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  3. ENH: Use pymdownx.superfences

    @effigies
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  4. FIX: Language for code block, missing comma

    @effigies
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Commits on Jul 9, 2019

  1. Drop modality-specific derivatives for now

    @effigies
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  2. Merge remote-tracking branch 'upstream/master' into common-derivatives

    @effigies
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  3. ENH: Restore derivative sub-BEPs to BEP list for now

    @effigies
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  4. FIX: Remove modality-specific files from mkdocs.yml

    @effigies
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Commits on Jul 15, 2019

  1. Apply suggestions from code review 

    Co-Authored-By: Franklin Feingold <35307458+franklin-feingold@users.noreply.github.com>
    @effigies @franklin-feingold
    effigies and franklin-feingold committed Jul 15, 2019
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Commits on Jul 16, 2019

  1. Apply suggestions from code review

    @effigies
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  2. FIX: Table alignment

    @effigies
    effigies committed Jul 16, 2019
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  3. FIX: Consistent list

    @effigies
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  4. FIX: Weird list style

    @effigies
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  5. Merge remote-tracking branch 'upstream/master' into common-derivatives

    @effigies
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  6. FIX: Weird list style

    @effigies
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Commits on Aug 14, 2019

  1. Merge remote-tracking branch 'upstream/master' into common-derivatives

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  2. FIX: Clarify naming derivatives after pipeline

    @effigies
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  3. RF: Abstract PipelineDescription.Container from Docker and Singularit… 

    …y-specific tags
    @effigies
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  4. Pacify linkchecker

    @effigies
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Commits on Aug 15, 2019

  1. [STY] Add missing table fence

    @oesteban @effigies
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Commits on Aug 22, 2019

  1. Merge remote-tracking branch 'upstream/master' into common-derivatives

    @effigies
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  2. [SPEC] Separate out imaging-specific "common derivatives"

    @effigies
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Commits on Sep 4, 2019

  1. ENH: Clarify data type, EEG examples, space/desc wording

    @effigies
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  2. [STY] Remove blank lines

    @effigies
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Commits on Sep 12, 2019

  1. Merge pull request #310 from effigies/common-imaging 

    [FIX] Separate out imaging-specific "common derivatives"
    @effigies
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  2. Merge remote-tracking branch 'upstream/master' into common-derivatives

    @effigies
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  3. MAINT: Update TOC, CODEOWNERS

    @effigies
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  4. ENH: Add language around non-compliant derivative datasets and files

    @effigies
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Commits on Sep 17, 2019

  1. STY: Drop double newline

    @effigies
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  2. STY: Fix link style

    @effigies
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Commits on Sep 18, 2019

  1. Update src/05-derivatives/01-introduction.md

    @effigies
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Commits on Oct 8, 2019

  1. Update src/02-common-principles.md

    @effigies
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  2. Merge pull request #334 from effigies/fix/relaxation 

    ENH: Clarify the position toward non-compliant derivative datasets and files
    @effigies
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  3. Merge branch 'master' into common-derivatives

    @effigies
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Commits on Oct 23, 2019

  1. specify further the pipeline following #345 

    #345  discuss splitting a pipeline into multiple derivatives with/without nesting
    Cyril Pernet committed Oct 23, 2019
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Commits on Oct 30, 2019

  1. Update src/05-derivatives/01-introduction.md 

    Co-Authored-By: Chris Markiewicz <markiewicz@stanford.edu>
    @effigies
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  2. Update src/05-derivatives/01-introduction.md 

    Co-Authored-By: Chris Markiewicz <markiewicz@stanford.edu>
    @effigies
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  3. Update src/05-derivatives/01-introduction.md 

    Co-Authored-By: Chris Markiewicz <markiewicz@stanford.edu>
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  4. Update src/05-derivatives/01-introduction.md 

    Co-Authored-By: Chris Markiewicz <markiewicz@stanford.edu>
    @effigies
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  5. Merge pull request #358 from bids-standard/CPernet-patch-1 

    specify further the pipeline following #345
    @effigies
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Commits on Nov 4, 2019

  1. Merge remote-tracking branch 'upstream/master' into common-derivatives

    @effigies
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  2. FIX: Links to coordinate system appendix

    @effigies
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Commits on Dec 5, 2019

  1. [FIX] Revise template-generated coordinate systems (#307) 

    * [FIX] Revise template-generated coordinate systems

This PR supersedes #213, and should be rebased with master after #306 is
merged.

W.r.t. master it only adds the table of _Nonstandard template
identifiers_

W.r.t. `common-derivatives`, the changes are:

  - [x] Removed the distinction between surface templates and volumetric
        templates. After all, to properly apply a surface template one
        should first spatially normalize to a particular volumetric
        template. Although it is possible to create mixed templates
        (e.g. using ``MNI152Lin`` to generate a mapping for volumetric
        coordinates and then, say, ``fsLR`` for the surface after some
        surface mapping process), this option should be discouraged.
        Anyways, this discussion does not affect how the names of BIDS
        entities should be specified, since one can always describe how
        the template coordinates are generated with the information
        described in this PR.
  - [x] Removed ``MNI152NLin6AsymConte69`` because it does not define
        any new coordinate system (see
        #207 (comment)),
  - [x] Removed ``FS305`` as it is now covered by ``fsaverage``.
  - [x] Reorganized subsections in "standard" vs "nonstandard" spaces.

* fix: added the concept of ``scanner`` as an Image-based coordinate system

- [x] Describes more clearly the situation when files do not have
``space-`` definition.
- [x] Remove the ``ReferenceIndex`` as an index does not generate a
coordinate system (the concept here is mixed up with that of  image
registration, which is just a process).
    @oesteban @effigies
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Commits on Dec 16, 2019

  1. Merge remote-tracking branch 'upstream/master' into common-derivatives

    @effigies
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Commits on Jan 29, 2020

  1. Merge remote-tracking branch 'upstream/master' into common-derivatives

    @effigies
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Commits on Feb 24, 2020

  1. Merge remote-tracking branch 'upstream/master' into common-derivatives

    @effigies
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  2. STY: Grey -> Gray

    @effigies
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Commits on Apr 2, 2020

  1. Update derivatives introduction with Oscar's suggestions 

    Co-Authored-By: Oscar Esteban <code@oscaresteban.es>
    @effigies @oesteban
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  2. Accept Oscar's suggestions for common data types 

    Co-Authored-By: Oscar Esteban <code@oscaresteban.es>
    @effigies @oesteban
    effigies and oesteban committed Apr 2, 2020
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Commits on Apr 17, 2020

  1. Merge remote-tracking branch 'upstream/master' into common-derivatives

    @effigies
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Commits on May 11, 2020

  1. BF: minor - mising _ before space following <source_keywords>

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Commits on May 20, 2020

  1. Merge remote-tracking branch 'upstream/master' into common-derivatives

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Commits on May 21, 2020

  1. FIX: Minor bugs

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Commits on May 22, 2020

  1. [ENH] Add res and den keywords to indicate resolution of resa… 

    …mpled data (#301)

* fix: force-push a rewrite addressing minimal changes

* sty: make linter happy

* [STY] Add missing table fence

* fix: force-push a rewrite addressing minimal changes

* sty: make linter happy

* Update src/05-derivatives/02-common-data-types.md

Co-Authored-By: Chris Markiewicz <effigies@gmail.com>

* Address @effigies' and @edickie's comments

* sty: fix missaligned table fence

* fix: better description for example following @edickie's comment

* More generalizable concepts (addressing @robertoostenveld's comments)

* Update src/05-derivatives/02-common-data-types.md

Co-Authored-By: Elizabeth DuPre <emd222@cornell.edu>

* Address @robertoostenveld's comment

* fix: ``res-<index>`` -> ``res-<label>`` + admonitions

* fix: cover one @effigies' suggestion

* remove unnecessary edit

* fix: example with bad formatting

* RF: Move res/den keywords to imaging derivatives

* REVERT Removal of example from Common Data Types

* Drop tip that does not match context

* STY: Satisfy linter

* enh: include @robertoostenveld's suggestion

* ENH: Add SpatialReference dictionary option and example

* STY: Drop parens

* Allow resolution/density to be a string or dictionary

* Eliminate dtseries.json example, add space-fsLR to avoid ambiguity

* Update src/05-derivatives/01-introduction.md

Co-authored-by: Oscar Esteban <code@oscaresteban.es>

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
Co-authored-by: Elizabeth DuPre <emd222@cornell.edu>
Co-authored-by: Christopher J. Markiewicz <markiewicz@stanford.edu>
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Commits on May 24, 2020

  1. MNT: Postpone thickness GIFTI example to structural derivatives

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  2. ENH: Apply Robert's suggestions

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  3. Update BIDSVersion in derivatives example JSON

    @effigies
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  4. ENH: Update wording for clarity

    @effigies
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  5. dparc -> dseg

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  6. STY: Drop quotes in dseg.tsv and reformat with spaces

    @effigies
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  7. Update link, conform RFC2119 terms

    @effigies
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  8. Use relative paths

    @effigies
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  9. Add resolution/density to masks and segmentations

    @effigies
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  10. STY: Typo

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Commits on May 25, 2020

  1. MNT: Drop admonition for now

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  2. Preface for individual/study templates

    @effigies
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Commits on May 26, 2020

  1. Revert to pre-derivatives description of XXXCoordinateSystem

    @effigies
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  2. FIX: Rename derivative directories to use <pipeline>-<variant>

    @effigies
    effigies committed May 26, 2020
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Commits on May 27, 2020

  1. Apply suggestions from code review 

    Co-authored-by: Robert Smith <robert.smith@florey.edu.au>
    @effigies @Lestropie
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  2. FIX: Clarify recommendation of desc to when no other entity suits

    @effigies
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  3. Update examples with T1w, events, EDF (EEG)

    @effigies
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  4. ENH: Drop "dictionary" for JSON "object"

    @effigies
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Commits on May 29, 2020

  1. Rename PipelineDescription to GeneratedBy, rework table and examples,… 

    … add description field
    @effigies
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  2. FIX: More dictionary -> object

    @effigies
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  3. Do not abbreviate abbreviation

    @effigies
    effigies committed May 29, 2020
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  4. Rename: keyword -> entity

    @effigies
    effigies committed May 29, 2020
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  5. Rewrite Sources description to clarify the A/B/C and X/Y/Z examples

    @effigies
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Commits on May 30, 2020

  1. More cleanup

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

    @effigies
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  3. Update src/05-derivatives/03-imaging.md 

    Co-authored-by: Satrajit Ghosh <satrajit.ghosh@gmail.com>
    @effigies @satra
    effigies and satra committed May 30, 2020
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Commits on Jun 1, 2020

  1. Reorganize derivatives

    @effigies
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  2. STY: Clean up links, formatting, outdated text

    @effigies
    effigies committed Jun 1, 2020
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  3. Fix link

    @effigies
    effigies committed Jun 1, 2020
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  4. Update TOC

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  5. Make dataset description example consistent with folder name example

    @effigies
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  6. Remove RawSources overlap with SpatialReference, some additional clar… 

    …ifying wording
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  7. ENH: Change single ROI binary image suffix from dseg to mask

    @effigies
    effigies committed Jun 1, 2020
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  8. Improve wording

    @effigies
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  9. Clarify discrete surface segmentations

    @effigies
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  10. Swap mapping/color and add an example dseg with new labels

    @effigies
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  11. Replace "tissue class" with more general "anatomical structure"

    @effigies
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  12. Add labels for masks

    @effigies
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  13. Update src/05-derivatives/03-imaging.md 

    Co-authored-by: Robert Smith <robert.smith@florey.edu.au>
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    effigies and Lestropie committed Jun 1, 2020
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  14. Fix section links, capitalization

    @effigies
    effigies committed Jun 1, 2020
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  15. Drop "Gray and White Matter" label

    @effigies
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  16. Drop extraneous line, make punctuation consistent

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Commits on Jun 2, 2020

  1. Missing paren

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Commits on Jun 3, 2020

  1. Apply suggestions from code review 

    Co-authored-by: Sanjula Madurapperuma <32578617+sanjulamadurapperuma@users.noreply.github.com>
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    effigies and sanjulamadurapperuma committed Jun 3, 2020
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  2. Apply suggestions from code review 

    Co-authored-by: Sanjula Madurapperuma <32578617+sanjulamadurapperuma@users.noreply.github.com>
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    effigies and sanjulamadurapperuma committed Jun 3, 2020
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  3. Update src/05-derivatives/03-imaging.md

    @effigies
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Commits on Jun 4, 2020

  1. Update src/05-derivatives/03-imaging.md

    @effigies
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  2. Update src/05-derivatives/03-imaging.md

    @effigies
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  3. Update src/05-derivatives/03-imaging.md 

    Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
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    satra and effigies committed Jun 4, 2020
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  4. ENH: Add RECOMMENDED DatasetType key to dataset description (#494)

    @effigies
    effigies committed Jun 4, 2020
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  5. Merge remote-tracking branch 'upstream/master' into common-derivatives

    @effigies
    effigies committed Jun 4, 2020
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