[ENH] Extend BIDS for Motion data (BEP029)

[JuliusWelzel]

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:

• @sjeung
• @JuliusWelzel

Links:

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

To do:

• revert 3c09175

[JuliusWelzel]

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]

@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

[JuliusWelzel]

Worked, thank you @sappelhoff

[sappelhoff]

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]

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

[sjeung]

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]

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]

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

…

On Wed, Mar 8, 2023 at 3:06 PM Sein Jeung ***@***.***> wrote: 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 <https://urldefense.com/v3/__https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html*chapter_L__;Iw!!Mih3wA!FuwouaChBW2-XoOm_JnIspL69eozUiLl3u4qgCGRBQiTvH86FcQ6pymqVP0k3UqrtSfVtY2tcVV06CW0sMi2DND3$> you have pointed to. As the purpose of HED is to describe the nature of events occurring in neuroimaging experiments, the first needed terms are for external body parts - though as HED includes "data feature" events (alpha burst, seizures, etc.) which are addressed in the SCORE library schema (built by Dora Hermes and Tal Pal Attia from the neurophysiologists' agreed on SCORE vocabulary), 'brain parts' should also be included - I need to check to what extent they are already represented in SCORE... Note that the HED vocabulary is structured as a set of term hierarchies (thus formed as, technically, a 'heterarchy'). For body parts, this should be simple (for example, "leg" under the DICOM term "pelvis and lower extremities", etc.). … <#m_-7070740569885242823_> On Sat, Mar 4, 2023 at 4:51 AM Remi Gau *@*.*> wrote: It would seem to me that the logical place to define hierarchies of body parts is in HED and not in BIDS per se. An anatomical library for HED is something I am thinking of and the hed working group has discussed. Within HED, the appropriate place for it might well be a subsidiary library schema that will attach to the base hed schema to avoid over bloating the base schema. Agreed that it would be best to rely on external "sources" for some sort of anatomical library. Ideally even better if kept in synch with the BodyPart examined metadata from DICOM as this is already the one used in BIDS for PET and microscopy. https://dicom.innolitics.com/ciods/cr-image/general-series/00180015 <https://urldefense.com/v3/__https://dicom.innolitics.com/ciods/cr-image/general-series/00180015__;!!Mih3wA!FuwouaChBW2-XoOm_JnIspL69eozUiLl3u4qgCGRBQiTvH86FcQ6pymqVP0k3UqrtSfVtY2tcVV06CW0sPcrspz0$> <https://urldefense.com/v3/https://dicom.innolitics.com/ciods/cr-image/general-series/00180015;!!Mih3wA!Hc0bHDP5WuxFQONK8FKdWfaNuIZ2vCRupiEQTEILNULUi45Bpa7wHBihk4k3cOg_wxkspFnmIMkZml19555NNkFM$ <https://urldefense.com/v3/__https://dicom.innolitics.com/ciods/cr-image/general-series/00180015__;!!Mih3wA!Hc0bHDP5WuxFQONK8FKdWfaNuIZ2vCRupiEQTEILNULUi45Bpa7wHBihk4k3cOg_wxkspFnmIMkZml19555NNkFM%24>> 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!FuwouaChBW2-XoOm_JnIspL69eozUiLl3u4qgCGRBQiTvH86FcQ6pymqVP0k3UqrtSfVtY2tcVV06CW0sMi2DND3$> <https://urldefense.com/v3/https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html*chapter_L;Iw!!Mih3wA!Hc0bHDP5WuxFQONK8FKdWfaNuIZ2vCRupiEQTEILNULUi45Bpa7wHBihk4k3cOg_wxkspFnmIMkZml1956z3dYo1$ <https://urldefense.com/v3/__https://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html*chapter_L__;Iw!!Mih3wA!Hc0bHDP5WuxFQONK8FKdWfaNuIZ2vCRupiEQTEILNULUi45Bpa7wHBihk4k3cOg_wxkspFnmIMkZml1956z3dYo1%24>> — 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$ <https://urldefense.com/v3/__https://github.com/bids-standard/bids-specification/pull/981*issuecomment-1454682475__;Iw!!Mih3wA!Hc0bHDP5WuxFQONK8FKdWfaNuIZ2vCRupiEQTEILNULUi45Bpa7wHBihk4k3cOg_wxkspFnmIMkZml195xBsVNbb%24>>, or unsubscribe <https://urldefense.com/v3/https://github.com/notifications/unsubscribe-auth/AKN2SFWO4V3XXRJU532MAZDW2MGDTANCNFSM5MNBXIIA;!!Mih3wA!Hc0bHDP5WuxFQONK8FKdWfaNuIZ2vCRupiEQTEILNULUi45Bpa7wHBihk4k3cOg_wxkspFnmIMkZml195ykucWhS$ <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AKN2SFWO4V3XXRJU532MAZDW2MGDTANCNFSM5MNBXIIA__;!!Mih3wA!Hc0bHDP5WuxFQONK8FKdWfaNuIZ2vCRupiEQTEILNULUi45Bpa7wHBihk4k3cOg_wxkspFnmIMkZml195ykucWhS%24>> . 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 <https://urldefense.com/v3/__https://github.com/smakeig__;!!Mih3wA!FuwouaChBW2-XoOm_JnIspL69eozUiLl3u4qgCGRBQiTvH86FcQ6pymqVP0k3UqrtSfVtY2tcVV06CW0sEI4uwwM$> for bringing up the points about and @Remi-Gau <https://urldefense.com/v3/__https://github.com/Remi-Gau__;!!Mih3wA!FuwouaChBW2-XoOm_JnIspL69eozUiLl3u4qgCGRBQiTvH86FcQ6pymqVP0k3UqrtSfVtY2tcVV06CW0sLU5j26W$> for the pointer, when we do get to work on the anatomical description project we will keep this in mind. — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/bids-standard/bids-specification/pull/981*issuecomment-1460797432__;Iw!!Mih3wA!FuwouaChBW2-XoOm_JnIspL69eozUiLl3u4qgCGRBQiTvH86FcQ6pymqVP0k3UqrtSfVtY2tcVV06CW0sM3MLgMx$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AKN2SFRC4B3XVMJXHWLDNB3W3DRC7ANCNFSM5MNBXIIA__;!!Mih3wA!FuwouaChBW2-XoOm_JnIspL69eozUiLl3u4qgCGRBQiTvH86FcQ6pymqVP0k3UqrtSfVtY2tcVV06CW0sNu-QIRG$> . 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

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]

+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]

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]

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]

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 :)