[ENH] Extend BIDS for Motion data (BEP029) by JuliusWelzel · Pull Request #981 · bids-standard/bids-specification

JuliusWelzel · 2022-01-20T15:26:21Z

Integrate BEP029 motion into the BIDS spec.

Link to HTML rendered BEP: https://bids-specification--981.org.readthedocs.build/en/981/modality-specific-files/motion.html

Leads:

Links:

examples: BEP029 Motion (examples) bids-examples#348
validator: https://github.com/bids-standard/bids-validator/pull/1434

To do:

revert 3c09175

[ENH] added changed in md from Sein

…ication into bep-029

JuliusWelzel · 2022-01-28T12:27:56Z

I think the extra file for the BEP is working fine however, some checks still do not pass. Maybe @sappelhoff can help us out here? Thanks :)

sappelhoff · 2022-01-28T12:53:11Z

@JuliusWelzel you can rebase your branch on master, or (easier) merge the commits from master into your branch. You are a few commits behind (6 commits, to be exact, see screenshot), and the issues of "linkchecker" have been fixed upstream :-)

PS: Let me know if you need help with that - I don't know how advanced your git knowledge is

…ication into bep-029

JuliusWelzel · 2022-01-28T13:32:04Z

Worked, thank you @sappelhoff

sappelhoff · 2023-03-08T16:52:32Z

This PR should also correct the text here:

bids-specification/src/modality-specific-files/near-infrared-spectroscopy.md

Lines 197 to 207 in 741d4ef

    
           All NIRS channels types MUST correspond to a [valid SNIRF data type](https://github.com/fNIRS/snirf/blob/master/snirf_specification.md#appendix). 
        
           Additional channels that are recorded simultaneously with the NIRS 
        
           device and stored in the same data file SHOULD be included as well. 
        
           However, additional channels that are  simultaneously recorded with a different device 
        
           SHOULD be stored according to their appropriate modality specification. 
        
           For example, motion data that was simultaneously recorded with a different device should be specified 
        
           according to BEP029 and not according to the NIRS data type. 
        
           Whereas, if the motion data was acquired in with the NIRS device itself, it should be included here with the NIRS data. 
        
           Any of the channel types defined in other BIDS specification MAY be used here as well such as `ACCEL` or `MAGN`. 
        
           As several of these data types are commonly acquired using NIRS devices they are included as an example at the base of the table. 
        
           Note that upper-case is REQUIRED.

☝️ the mention of BEP029 should be adjusted to refer to the BIDS Motion modality instead.

sappelhoff

see: #981 (comment)

sappelhoff · 2023-03-08T16:54:54Z

src/modality-specific-files/motion.md

+Restricted keyword list for column `type` in alphabetic order.
+Note that upper-case is REQUIRED:


not a blocker for merging this PR, but before release, we must clarify how channel types are shared between modalities. I have opened a new issue for this:

Formalize how channel types are shared between modalities that use channels.tsv files. #1436

…ication into bep-029

sjeung · 2023-03-08T20:05:54Z

Details

Remi - Thanks for the useful note. Currently, the HED vocabulary for body parts is haphazard, but it should be straightforward to build out a structured (external) body part HED "library schema" from the DICOM BodyPart vocabulary https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L you have pointed to. As the purpose of HED is to describe the nature of events occurring in neuroimaging experiments, the first needed terms are for external body parts - though as HED includes "data feature" events (alpha burst, seizures, etc.) which are addressed in the SCORE library schema (built by Dora Hermes and Tal Pal Attia from the neurophysiologists' agreed on SCORE vocabulary), 'brain parts' should also be included - I need to check to what extent they are already represented in SCORE... Note that the HED vocabulary is structured as a set of term hierarchies (thus formed as, technically, a 'heterarchy'). For body parts, this should be simple (for example, "leg" under the DICOM term "pelvis and lower extremities", etc.).
…
On Sat, Mar 4, 2023 at 4:51 AM Remi Gau @.> wrote: It would seem to me that the logical place to define hierarchies of body parts is in HED and not in BIDS per se. An anatomical library for HED is something I am thinking of and the hed working group has discussed. Within HED, the appropriate place for it might well be a subsidiary library schema that will attach to the base hed schema to avoid over bloating the base schema. Agreed that it would be best to rely on external "sources" for some sort of anatomical library. Ideally even better if kept in synch with the BodyPart examined metadata from DICOM as this is already the one used in BIDS for PET and microscopy. https://dicom.innolitics.com/ciods/cr-image/general-series/00180015 <https://urldefense.com/v3/https://dicom.innolitics.com/ciods/cr-image/general-series/00180015;!!Mih3wA!Hc0bHDP5WuxFQONK8FKdWfaNuIZ2vCRupiEQTEILNULUi45Bpa7wHBihk4k3cOg_wxkspFnmIMkZml19555NNkFM$> https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L <https://urldefense.com/v3/https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html*chapter_L;Iw!!Mih3wA!Hc0bHDP5WuxFQONK8FKdWfaNuIZ2vCRupiEQTEILNULUi45Bpa7wHBihk4k3cOg_wxkspFnmIMkZml1956z3dYo1$> — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/https://github.com/bids-standard/bids-specification/pull/981*issuecomment-1454682475;Iw!!Mih3wA!Hc0bHDP5WuxFQONK8FKdWfaNuIZ2vCRupiEQTEILNULUi45Bpa7wHBihk4k3cOg_wxkspFnmIMkZml195xBsVNbb$>, or unsubscribe <https://urldefense.com/v3/https://github.com/notifications/unsubscribe-auth/AKN2SFWO4V3XXRJU532MAZDW2MGDTANCNFSM5MNBXIIA;!!Mih3wA!Hc0bHDP5WuxFQONK8FKdWfaNuIZ2vCRupiEQTEILNULUi45Bpa7wHBihk4k3cOg_wxkspFnmIMkZml195ykucWhS$> . You are receiving this because you were mentioned.Message ID: @.>
-- Scott Makeig, Research Scientist and Director, Swartz Center for Computational Neuroscience, Institute for Neural Computation, University of California San Diego, La Jolla CA 92093-0559, http://sccn.ucsd.edu/~scott

Thank you @smakeig for bringing up the points about and @Remi-Gau for the pointer, when we do get to work on the anatomical description project we will keep this in mind.

sjeung · 2023-03-08T20:06:34Z

This PR should also correct the text here:

bids-specification/src/modality-specific-files/near-infrared-spectroscopy.md

Lines 197 to 207 in 741d4ef

All NIRS channels types MUST correspond to a [valid SNIRF data type](https://github.com/fNIRS/snirf/blob/master/snirf_specification.md#appendix).

Additional channels that are recorded simultaneously with the NIRS

device and stored in the same data file SHOULD be included as well.

However, additional channels that are simultaneously recorded with a different device

SHOULD be stored according to their appropriate modality specification.

For example, motion data that was simultaneously recorded with a different device should be specified

according to BEP029 and not according to the NIRS data type.

Whereas, if the motion data was acquired in with the NIRS device itself, it should be included here with the NIRS data.

Any of the channel types defined in other BIDS specification MAY be used here as well such as `ACCEL` or `MAGN`.

As several of these data types are commonly acquired using NIRS devices they are included as an example at the base of the table.

Note that upper-case is REQUIRED.

☝️ the mention of BEP029 should be adjusted to refer to the BIDS Motion modality instead.

Updated now : )

smakeig · 2023-03-08T20:09:55Z

The HED Working Group would be happy to assist or collaborate in an effort to build out a HED body-parts library schema ... Do discuss with us, write me or ***@***.*** to discuss, perhaps at our twice-weekly Working Group meetings. Scott

…

-- Scott Makeig, Research Scientist and Director, Swartz Center for Computational Neuroscience, Institute for Neural Computation, University of California San Diego, La Jolla CA 92093-0559, http://sccn.ucsd.edu/~scott

src/modality-specific-files/near-infrared-spectroscopy.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

…ication into bep-029

src/modality-specific-files/motion.md

critical aspects were addressed

sappelhoff

+1 for merging, and we can smooth out things (in particular the channel types situation) before a release with smaller, dedicated PRs.

JuliusWelzel · 2023-03-16T09:13:16Z

+1 for merging, and we can smooth out things (in particular the channel types situation) before a release with smaller, dedicated PRs.

I was just about to revert the added column int the channel type table, but happy to push that to the main branch

sappelhoff · 2023-03-16T09:25:18Z

I was just about to revert the added column int the channel type table, but happy to push that to the main branch

let's wait with how the channel types discussion progresses 👍

sappelhoff · 2023-03-17T08:47:50Z

I got some more approvals for this in the maintainers channel, so I will merge this now and we will keep working on it until the release of BIDS 1.9.0.

Congrats to @sjeung and @JuliusWelzel and your team for the work up to this point! 🎉

Looking forward to the release!

sjeung · 2023-03-17T08:52:23Z

I got some more approvals for this in the maintainers channel, so I will merge this now and we will keep working on it until the release of BIDS 1.9.0.

Congrats to @sjeung and @JuliusWelzel and your team for the work up to this point! 🎉

Looking forward to the release!

Thank you so much everyone! It's been awesome working on this extension. We will stay involved for further improvements and maintenance of the spec :)

JuliusWelzel and others added 8 commits January 10, 2022 21:41

[ENH] init commit for the BEP029 specification

f3f2199

[ENH] first complete draft of the BEP029 md

d6b8ee3

[ENH] updated draft after discussion with Sein

0559356

_tracksys key in _motion.tsv file name is required

b637b09

Modified initial section to match style of other extensions.

459ec4f

Added field "MissingValues" in motion.json

2bec555

Merge pull request #1 from sjeung/bep-029

238a225

[ENH] added changed in md from Sein

Merge branch 'bids-standard:master' into bep-029

e6d8866

sappelhoff added the BEP label Jan 20, 2022

JuliusWelzel added 7 commits January 28, 2022 13:00

[FIX] 29-motion.md now checks

ae8e5ef

Merge branch 'bep-029' of https://github.com/JuliusWelzel/bids-specif…

089b7e3

…ication into bep-029

'STY: Fixed Markdown style'

4037578

[FIX] typos

7b12520

[FIX] typos

fc7a22e

'STY: Fixed Markdown style'

a0c186b

'STY: Fixed Markdown style'

52163f1

JuliusWelzel and others added 11 commits January 28, 2022 14:16

fetch upstream

9152e99

[ENH] init commit for the BEP029 specification

1817738

[ENH] first complete draft of the BEP029 md

2d8b536

[ENH] updated draft after discussion with Sein

eeebe86

_tracksys key in _motion.tsv file name is required

f11444d

Modified initial section to match style of other extensions.

8f2b3aa

Added field "MissingValues" in motion.json

fca295b

[FIX] 29-motion.md now checks

0afbe2a

'STY: Fixed Markdown style'

f790935

Merge branch 'bep-029' of https://github.com/JuliusWelzel/bids-specif…

bd3dc1c

…ication into bep-029

Merge branch 'bids-standard:master' into bep-029

5c75434

sappelhoff previously requested changes Mar 8, 2023

View reviewed changes

sappelhoff reviewed Mar 8, 2023

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sjeung added 2 commits March 8, 2023 21:02

Mention of BEP 029 changed to BIDS-motion

00bb112

Merge branch 'bep-029' of https://github.com/JuliusWelzel/bids-specif…

3f9345e

…ication into bep-029

sappelhoff reviewed Mar 8, 2023

View reviewed changes

src/modality-specific-files/near-infrared-spectroscopy.md Outdated Show resolved Hide resolved

sjeung and others added 8 commits March 8, 2023 23:21

Update src/modality-specific-files/near-infrared-spectroscopy.md

b55338e

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

Merge branch 'bids-standard:master' into bep-029

38f38f7

update contributor emojis

03e6bad

Typo correction

dac3d7c

Merge branch 'bep-029' of https://github.com/JuliusWelzel/bids-specif…

825ccc6

…ication into bep-029

Update near-infrared-spectroscopy.md

fdfd89c

update channels type table

91342c7

Merge branch 'master' into bep-029

dcaebd7

sappelhoff reviewed Mar 15, 2023

View reviewed changes

src/modality-specific-files/motion.md Outdated Show resolved Hide resolved

misc fixes

f613ba7

sappelhoff approved these changes Mar 16, 2023

View reviewed changes

sappelhoff merged commit 843f450 into bids-standard:master Mar 17, 2023

sappelhoff mentioned this pull request Mar 17, 2023

BEP029: Extend BIDS to add motion capture and movement data #443

Closed

sappelhoff changed the title ~~BEP029 Motion (spec)~~ [ENH] Extend BIDS for Motion data (BEP029) Mar 17, 2023

JuliusWelzel deleted the bep-029 branch March 17, 2023 09:33

shnizzedy mentioned this pull request Oct 13, 2023

BEP 012: Functional MRI derivatives #519

Draft

		Restricted keyword list for column `type` in alphabetic order.
		Note that upper-case is REQUIRED:

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