[ENH] Derived (processed) MR data by chrisgorgo · Pull Request #109 · bids-standard/bids-specification

chrisgorgo · 2018-12-16T20:17:08Z

This PR culminates over two years of discussions and work on BIDS Derivatives. I derived it from our RC1 Google Document with the following changes:

I removed the Space JSON metadata field - it was never properly described and seemed redundant with ReferenceMap
I opted not to include the transformation files specification in this PR. Without specifying what file format to use to store transformations it has limited use - hopefully, it could be added later in another PR.
I replaced desc-manual restricted key/value pair with a JSON field (for segmentation)
I limited the file formats for surface data to GIFTI or CIFTI (previously they were only recommended which lead to too much flexibility).
I stipulated for label to use Abbreviation in the context of segmentation metadata (instead of index, context or name which was too flexible)
I opted not to include qform/sform in tractography metadata in this PR since it seems not well described and quite controversial.
Similarly, I could not find a proper description for Param1, Param2 etc. so I also left them out.
Limited allowed suffixes for the scalar derivatives.

Calling @effigies @satra @sgiavasis @oesteban @edickie @francopestilli @nicholst @tyarkoni @ahoopes for validation and comments. Please send suggestions via PRs to https://github.com/chrisfilo/bids-specification/tree/enh/derivatives.

I'll try to work on examples and the validator over the xmas break. Many thanks to everyone who contributed to this work.

arokem

A few small comments on the dMRI part.

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

src/05-derivatives/01-introduction.md

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

Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>

…into enh/derivatives

…ication into enh/space_examples

oesteban · 2019-03-29T18:02:55Z

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

 | MNI152Lin                                           | Also known as ICBM (version with linear coregistration) [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin)                                                                                                                                                                                       |
-| MNI152NLin6\[Sym&#124;Asym\]                        | Also known as ICBM 6th generation (non-linear coregistration). Used by SPM99 -   SPM8 and FSL (MNI152NLin6Sym). [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6)                                                                                                                           |
+| MNI152NLin6\[Sym&#124;Asym\]                        | Also known as ICBM 6th generation (non-linear coregistration). Used by SPM99 - SPM8 and FSL (MNI152NLin6Sym). [http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6](http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6)                                                                                                                             |
+| MNI152NLin6AsymConte69                              | Template based on MNI152NLin6Asym using Conte69 data. Built by Human Connectome Project. [https://github.com/Washington-University/HCPpipelines/tree/master/global/templates](https://github.com/Washington-University/HCPpipelines/tree/master/global/templates)                                                                                                |


IMHO This should be fsLR. Space has no notion of surfaces or volumes.

If you think fsLR for this volume space defined by a volume template would be more intuitive we can change it. Pinging @edickie for second opinion.

I dunno, I don't really know MNI152NLin6AsymConte69 (I actually just register to MNI152NLin6Sym in my workflows anyway..)

oesteban · 2019-03-29T18:05:50Z

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

 | Coordinate System                                   | Description                                                                                                                                                                                                                                                                                                                                                      |
-| ---------------------------------------------------   | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------   |
+| --------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| FS305                                               | FreeSurfer variant of the MNI305 space                                                                                                                                                                                                                                                                                                                           |


This should be implicit to fsaverage* for the same reasons of MNI152NLin6AsymConte69 should not be a space. This example clearly shows how sampling should be detached from the notion of space.

This is just a label, but it should not include any special character (such as *), so if anything fsaverage can be used. I not familiar with this space though - @edickie did you add this one?

[ENH] replacing `CoordinateSystem` replacement with `space` + examples

effigies

Inconsistencies with L221.

effigies · 2019-04-04T15:41:14Z

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

+pipeline/
+    sub-001/
+        anat/
+            sub-001_hemi-L_dparc.label.gii


Suggested change

sub-001_hemi-L_dparc.label.gii

sub-001_hemi-L_dseg.label.gii

effigies · 2019-04-04T15:41:22Z

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

+    sub-001/
+        anat/
+            sub-001_hemi-L_dparc.label.gii
+            sub-001_hemi-R_dparc.label.gii


Suggested change

sub-001_hemi-R_dparc.label.gii

sub-001_hemi-R_dseg.label.gii

effigies · 2019-04-04T15:41:33Z

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

+pipeline/
+    sub-001/
+        anat/
+            sub-001_dparc.dlabel.nii


Suggested change

sub-001_dparc.dlabel.nii

sub-001_dseg.dlabel.nii

effigies · 2019-04-04T15:41:41Z

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

+    sub-001/
+        anat/
+            sub-001_dparc.dlabel.nii
+            sub-001_dparc.dlabel.nii


Suggested change

sub-001_dparc.dlabel.nii

sub-001_dseg.dlabel.nii

Yeah. I think there is a history of referring to atlases in nifti as segmentation and atlases on the surface as parcellations, so _dseg and _dparc suffixes appeared. but I agree that there is no reason for this.

oesteban · 2019-04-10T23:04:15Z

Hi @bids-standard/bep_leads, would it make sense to merge this PR into a branch under the upstream repo so @sappelhoff has better handles over the conversation (in a new PR)? WDYT @chrisgorgo, wouldn't that release you from moderating this PR?

chrisgorgo · 2019-04-12T03:06:42Z

Yes this would indeed facilitate someone else taking over chaperoning this PR. Happy to facilitate this process if someone wants to take over. Best, Chris

…

On Wed, Apr 10, 2019 at 4:04 PM Oscar Esteban ***@***.***> wrote: Hi @bids-standard/bep_leads <https://github.com/orgs/bids-standard/teams/bep_leads>, would it make sense to merge this PR into a branch under the upstream repo so @sappelhoff <https://github.com/sappelhoff> has better handles over the conversation (in a new PR)? WDYT @chrisgorgo <https://github.com/chrisgorgo>, wouldn't that release you from moderating this PR? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#109 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAOkpwrW-dbGikSyPb4R0pqwNbxEnrZgks5vfm3xgaJpZM4ZVavQ> .

sappelhoff · 2019-04-12T07:04:07Z

I have just pushed a fresh "derivatives" branch to our bids-standard/bids-specification repo. We could merge this present branch into derivatives (i.e., change the "base" of this PR and then merge it)

I'd prefer if @chrisgorgo could do that however, because there is this scary warning:

Then once we have changed base and merged this PR, we can make a new PR from the derivatives branch into master and I can keep that PR up to date.

effigies · 2019-04-12T14:23:45Z

Updated the base branch. @chrisfilo, if you can resolve conflicts, we can get this off your plate.

effigies · 2019-04-12T14:47:43Z

@sappelhoff I didn't see your request that @chrisgorgo do the base change. Very sorry about that.

…into enh/derivatives

chrisgorgo added 5 commits December 16, 2018 11:41

Adding derivatives

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adding derivatives to the index

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chrisgorgo added enhancement New feature or request functional MRI structural MRI labels Dec 16, 2018

chrisgorgo added 2 commits December 16, 2018 12:21

fixed links

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This was referenced Dec 27, 2018

Documenting the contrast suffix and disambiguating it from the catch-all modality categorization #119

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[WIP] adding first BEP010 spec #118

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template cleanup

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Co-Authored-By: chrisfilo <krzysztof.gorgolewski@gmail.com>

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

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…into enh/derivatives

syntax fixes

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remove old extensions

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chrisgorgo added 10 commits March 20, 2019 15:38

Merge branch 'enh/derivatives' into enh/space_examples

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

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…ication into enh/space_examples

fixes

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adding desc to structural derivatives

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Merge branch 'enh/derivatives' into enh/space_examples

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anat->native + cleanup

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cleaning leftover anat's

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fix syntax

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clarify links between raw and derived datasets

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chrisgorgo mentioned this pull request Mar 22, 2019

[MISC] Add bep006 and bep010 to completed beps and fix links #186

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native -> individual

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add volspace for meshes

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ReferenceMap -> SpatialReference

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Merge pull request #12 from chrisfilo/enh/space_examples

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[ENH] replacing `CoordinateSystem` replacement with `space` + examples

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effigies changed the base branch from master to derivatives April 12, 2019 14:21

effigies mentioned this pull request Apr 12, 2019

Proposal: BEP PRs should come from branches on the main repository #203

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

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chrisgorgo merged commit dd7f997 into bids-standard:derivatives Apr 14, 2019

effigies mentioned this pull request Apr 16, 2019

[ENH] Derived (processed) MR data #207

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oesteban commented Apr 10, 2019

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chrisgorgo commented Dec 16, 2018 •

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