BEP25 - Working solution for spine scans

[Thomas Nichols]

Dear Jose & Maria and below-the-neck-BIDS-folk,

Thanks for kicking off work on BEP25, on extending BIDS to other brain regions.  As it happens, I'm involved in a project that also has spine data.  Since there are often multiple spine scans collected at the same time (alongside brain), we've looked to your BEP to see how we could distinguish the body parts.

While I see your BEP proposes a new tag, "bp" for bodypart, we want to work within the existing BIDS framework for now.  Hence we've taken to using the acquisition tag (acq) to label with the body part, with bodypart names drawn (as you suggest) from Body Part Examined DICOM tag, and I assume the table of permitted values (Annex L “Correspondence of Anatomic Region Codes and Body Part Examined Defined Terms”).

It would lead to file names with portions:  "acq-Spine", "acq-CervicalSpine", "acq-ThoracicSpine".  See below for the spine-related portions of Annex L).

I'm writing to solicit input from yourselves and the greater BIDS community about the advisability of this interim solution.  

-Tom

Coding Scheme Designator	Code Value	Code Meaning	Body Part Examined	SNOMED-RT ID (Retired)	BIDS Proposed
SCT	122494005	Cervical spine	CSPINE	T-11501	CervicalSpine
SCT	297171002	Cervico-thoracic spine	CTSPINE	T-D00F7	CervicoThoracicSpine
SCT	122496007	Lumbar spine	LSPINE	T-11503	LumbarSpine
SCT	297173004	Lumbo-sacral spine	LSSPINE	T-D00F9	LumboSacralSpine
SCT	39723000	Sacroiliac joint	SIJOINT	T-15680	SacroiliacJoint
SCT	54735007	Sacrum	SSPINE	T-11AD0	Sacrum
SCT	421060004	Spine	SPINE	T-D04FF	Spine
SCT	122495006	Thoracic spine	TSPINE	T-11502	ThoracicSpine
SCT	297172009	Thoraco-lumbar spine	TLSPINE	T-D00F8	ThoracoLumbarSpine

__________________________________________________________

Thomas Nichols, PhD

Professor of Neuroimaging Statistics

Nuffield Department of Population Health | University of Oxford
Big Data Institute | Li Ka Shing Centre for Health Information and Discovery
Old Road Campus | Headington | Oxford | OX3 7LF | United Kingdom
T: +44 1865 743590 | E: thomas....@bdi.ox.ac.uk
W: http://nisox.org | http://www.bdi.ox.ac.uk

[saborit...@externos.gva.es]

Dear Tom,

Sorry for answering late and thanks for thinking about giving our
opinion on this adaptation.

We believe that the use of "acq-" like body part tagging is the best
option to work with these images and maintain the BIDS essence. On the
other hand, maybe another way of labeling is not possible in BIDS, so
this method is the only way.

If you need anything, do not hesitate to contact us.

Best regards,

Jose Manuel Saborit Torres.


Thomas Nichols <thomas....@bdi.ox.ac.uk> escribió:

> Dear Jose & Maria and below-the-neck-BIDS-folk,
>
> Thanks for kicking off work on BEP25, on extending BIDS to other brain
> regions. As it happens, I'm involved in a project that also has spine
> data. Since there are often multiple spine scans collected at the same
> time (alongside brain), we've looked to your BEP to see how we could
> distinguish the body parts.
>
> While I see your BEP proposes a new tag, "bp" for bodypart, we want to
> work within the existing BIDS framework for now. Hence we've taken to
> using the acquisition tag (acq) to label with the body part, with bodypart
> names drawn (as you suggest) from Body Part Examined

> <https://dicom.innolitics.com/ciods/raw-data/general-series/00180015> DICOM

> tag, and I assume the table of permitted values (Annex L “Correspondence of
> Anatomic Region Codes and Body Part Examined Defined Terms”

> <http://dicom.nema.org/medical/dicom/current/output/chtml/part16/chapter_L.html#chapter_L>

> ).
>
> It would lead to file names with portions: "acq-Spine",
> "acq-CervicalSpine", "acq-ThoracicSpine". See below for the spine-related
> portions of Annex L).
>
> I'm writing to solicit input from yourselves and the greater BIDS community
> about the advisability of this interim solution.
>
> -Tom
>
>
> Coding Scheme Designator Code Value Code Meaning Body Part Examined SNOMED-RT
> ID (Retired) BIDS Proposed

> SCT 122494005 <http://snomed.info/id/122494005> Cervical spine CSPINE
> T-11501 CervicalSpine
> SCT 297171002 <http://snomed.info/id/297171002> Cervico-thoracic spine
> CTSPINE T-D00F7 CervicoThoracicSpine
> SCT 122496007 <http://snomed.info/id/122496007> Lumbar spine LSPINE T-11503
> LumbarSpine
> SCT 297173004 <http://snomed.info/id/297173004> Lumbo-sacral spine LSSPINE
> T-D00F9 LumboSacralSpine
> SCT 39723000 <http://snomed.info/id/39723000> Sacroiliac joint SIJOINT
> T-15680 SacroiliacJoint
> SCT 54735007 <http://snomed.info/id/54735007> Sacrum SSPINE T-11AD0 Sacrum
> SCT 421060004 <http://snomed.info/id/421060004> Spine SPINE T-D04FF Spine
> SCT 122495006 <http://snomed.info/id/122495006> Thoracic spine TSPINE
> T-11502 ThoracicSpine
> SCT 297172009 <http://snomed.info/id/297172009> Thoraco-lumbar spine TLSPINE

[Thomas Nichols]

Super! Thanks... we're moving ahead with the "acq" approach for now.  Looking forward to see BEP25 move ahead.

-Tom

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[Chris Markiewicz]

The Microscopy BEP (https://bids.neuroimaging.io/bep031) is also considering how to encode anatomical structures. It looks like they're using "Organ" and "Location" metadata fields, and haven't proposed an entity.

Just a heads up in case there's duplicated effort being made along two fronts.

Chris

[Marie-Helene Bourget]

Hi everyone!

Thanks Chris for bringing this discussion to our attention.

In the Microscopy BEP, each sample is identified in the filename with a unique label. Because of that, there is no need for a specific entity in the filename to distinguish between different images of the same subject.

However, this is a question we examined before, and we also thought that people could use the “acq” entity if they wanted to track that information in the filename without it being obligatory (as mentioned in our FAQ: https://docs.google.com/document/d/1Nlu6QVQrbOQtdtcRarsONbX5SrOubXWBvkV37LRRqrc/edit#heading=h.4k5zzopnsbd9).

Best,

Marie-Hélène

[Mastaneh Torkamani]

Dear all

I'm re-opening this discussion about inclusion of body parts since development of BEP25 seems to have stopped. 

In a dataset that contains not only in vivo MRI but also ex vivo MRI and multiple microscopy modalities from different brain regions (cortex, hippocampus, or right and left hemispheres), 

what are the recommendations or practices for organizing the raw data while keeping the file levels consistent while keeping different body parts and scans separate? 

For example, 

sub-<label> /

     ses-exvivo /

          bp-<bodypart> /

               anat /

               dwi /

               micr /

or 

sub-<label>

    exvivoMRI (or ses-exvivoMRI?)

     acq-<bodypart> or bp-<bodypart>|

[anat, dwi, etc.]

    micr

acq-<bodypart> or bp-<bodypart>

              [BF, CONF, FLUO] or rather [IHC, nissl, myelin, etc.]?

Thank you in advance for any tips,

Mastaneh 

[Oostenveld, R. (Robert)]

Dear Mastaneh

I suggest you study the microscopy section of the BIDS specification. It prescribes that there are directory levels sub-xx/ses-xx/ followed by modality. So neither bp-xxx nor aq-xxx is permitted as directory level, but acq-xxx can be part of the filename. Furthermore, sample-xxx is required to be part of the filename (for microscopy, not for anatomical MRI).

The BodyPart and BodyPartDetails are coded in the json file (see https://bids-specification.readthedocs.io/en/stable/modality-specific-files/microscopy.html#sample), not in the file name nor in the directory name.

best regards,

Robert

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