[MISC] Clarify participant_id in participants.tsv file if it exists #738

adam2392 · 2021-02-18T02:29:41Z

Closes: #737

Question: "In case of single-session studies, this file has one compulsory column participant_id that consists of sub-, followed by a list of optional columns describing participants. " is in the current spec.

What does that mean? In case of single-session studies? Does that mean in single-session studies, this file is compulsory with participant_id a certain way?

sappelhoff · 2021-02-18T08:35:26Z

Thanks for taking a stab at this @adam2392 --> I think it's good to clarify it.

With regards to your question --> I have no clue. Perhaps the other @bids-standard/maintainers know.

I had a look at the Longitudinal and multi-site studies section to see whether it clarifies things, but I think it should rather be clarified itself (using SHOULD / MUST terminology).

Let me give a few examples of what I think should change:

Session label ~~can~~ MUST consist only of alphanumeric characters [a-zA-Z0-9] and ~~should~~ SHOULD be consistent across subjects.
If numbers are used in session labels we ~~recommend~~ RECOMMEND using zero padding
Acquisition time of session can be defined in the sessions file ~~(see below for details)~~ [insert markdown link for "sessions file"]
The extra session layer (at least one /ses- subfolder) ~~should~~ MUST be added for all subjects if at least one subject in the dataset has more than one session. ~~Skipping the session layer for only some subjects in the dataset is not allowed.~~

And then under Sessions file I find it confusing that the text refers to a "participant key file" ... probably, sessions.tsv is meant by that, so that should be clarified as well IMHO

In case of multiple sessions there is an option of adding additional participant key files describing variables changing between sessions. In such case one file per participant should be added. These files need to include compulsory session_id column and describe each session by one and only one row. Column names in per participant key files have to be different from group level participant key column names.

adam2392 · 2021-02-22T16:33:46Z

@sappelhoff

addressed all your comments, and
assuming the participants.tsv file is always RECOMMENDED, I added explicit language to clarify the question I had.

sappelhoff · 2021-02-22T16:44:48Z

src/06-longitudinal-and-multi-site-studies.md

-The extra session layer (at least one `/ses-<label>` subfolder) should
+The extra session layer (at least one `/ses-<label>` subfolder) SHOULD
 be added for all subjects if at least one subject in the dataset has more than
-one session. Skipping the session layer for only some subjects in the dataset is
-not allowed. If a `/ses-<label>` subfolder is included as part of the
-directory hierarchy, then the same `ses-<label>` tag must also be
+one session. If a `/ses-<label>` subfolder is included as part of the
+directory hierarchy, then the same `ses-<label>` tag MUST also be


Skipping the session layer for only some subjects in the dataset is
not allowed

I actually think that the original text here meant to say that:

The extra session layer (at least one /ses-<label> subfolder) MUST
be added for all subjects if at least one subject in the dataset has more than
one session.

instead of the SHOULD you used here.

opinions @Remi-Gau @tsalo ?

on the other hand, that doesn't really make sense, because there are experiments where some subjects perform an extra session 🤔

I think skipping the ses-<X> in some subjects is allowed if say not all subjects have the same sessions. Rn this results in a warning in validator, which basically all my data has this warning :p.

Re MUST vs SHOULD:

The extra session layer (at least one /ses-<label> subfolder) MUST be added for all subjects if at least one subject in the dataset has more than one session.

seems reasonable to me... The problem is how does one validate this? If one has multiple "sessions" per subject, then that implies there are potentially different electrode/channels across those sessions, so the user would want to store it as such. Does this basically mean if one has:

sub-01/ sub-01_ses-01_task-blah_ieeg.vhdr ...

it's allowed, but if you have:

sub-01/ sub-01_ses-01_task-blah_ieeg.vhdr sub-01_ses-02_task-blah_ieeg.vhdr ...

it's not?

I think skipping the ses- in some subjects is allowed if say not all subjects have the same sessions. Rn this results in a warning in validator, which basically all my data has this warning

yes, I experienced that warning multiple times myself 🙄 I think this case is more common than thought when this warning was originally implemented. That is, more often it's a choice, rather than an overlooked error.

re: your example --> yes 🤔 but I think your current changes (apart from my comments below) are actually fine and clarify the situation without changing the state of anything (which is what we should aim for), so I'd be fine with leaving the SHOULD, not interpreting it as a MUST post-hoc.

So basically turning it into a MUST would make the following non-BIDS, correct?

├── sub-1 │ └── eeg └── sub-2 ├── ses-1 │ └── eeg └── ses-2 └── fmri

yes, that's how I interpret it as well. What's annoying is that first the text says "should" (not MUST), and then the follow up sentence is:

Skipping the session layer for only some subjects in the dataset is not allowed.

so basically the "should" is actually a MUST.

However:

I am not sure why this rule makes sense

I am pretty sure that I have seen datasets not conforming to this rule

There is no validator support for this rule as far as I know

🙄 perhaps we can discuss this tonight in the maintainers meeting

Yeah the inconsistency should be fixed or clarified.

I mean I find the folder structure I described above "ugly", but thank goodness we don't just rely on my sense of aesthetics.

😉

src/06-longitudinal-and-multi-site-studies.md

src/03-modality-agnostic-files.md

src/06-longitudinal-and-multi-site-studies.md

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

src/06-longitudinal-and-multi-site-studies.md

sappelhoff · 2021-03-01T08:36:04Z

src/06-longitudinal-and-multi-site-studies.md

-The extra session layer (at least one `/ses-<label>` subfolder) should
+The extra session layer (at least one `/ses-<label>` subfolder) SHOULD
 be added for all subjects if at least one subject in the dataset has more than
-one session. Skipping the session layer for only some subjects in the dataset is
-not allowed. If a `/ses-<label>` subfolder is included as part of the
-directory hierarchy, then the same `ses-<label>` tag must also be
+one session. If a `/ses-<label>` subfolder is included as part of the
+directory hierarchy, then the same `ses-<label>` tag MUST also be


I think skipping the ses- in some subjects is allowed if say not all subjects have the same sessions. Rn this results in a warning in validator, which basically all my data has this warning

yes, I experienced that warning multiple times myself 🙄 I think this case is more common than thought when this warning was originally implemented. That is, more often it's a choice, rather than an overlooked error.

re: your example --> yes 🤔 but I think your current changes (apart from my comments below) are actually fine and clarify the situation without changing the state of anything (which is what we should aim for), so I'd be fine with leaving the SHOULD, not interpreting it as a MUST post-hoc.

src/06-longitudinal-and-multi-site-studies.md

tsalo

Some minor wording/formatting requests.

src/03-modality-agnostic-files.md

src/06-longitudinal-and-multi-site-studies.md

Co-authored-by: Taylor Salo <tsalo006@fiu.edu>

tsalo

The changes look good to me. Thanks!

effigies

LGTM. Only remaining suggestion is to split sentences with newlines.

src/03-modality-agnostic-files.md

src/06-longitudinal-and-multi-site-studies.md

sappelhoff · 2021-03-03T09:07:44Z

Thanks @adam2392!

Adding clarification.

d6a8ff0

adam2392 requested a review from sappelhoff February 18, 2021 02:29

adam2392 added 2 commits February 22, 2021 11:30

Fix clarifications.

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Fix link.

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

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sappelhoff requested review from tsalo and Remi-Gau March 1, 2021 08:37

Add link back.

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[MISC] Clarify participant_id in participants.tsv file if it exists #738

[MISC] Clarify participant_id in participants.tsv file if it exists #738

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[MISC] Clarify participant_id in participants.tsv file if it exists #738

[MISC] Clarify participant_id in participants.tsv file if it exists #738

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