Placement of experimental notes in BIDS tree

[Joshua Teves]

Hello,

I would like to include some experimental notes for my data, such as, "Subject expressed discomfort" in the BIDS tree. It's unclear where that should go, since it seems that it would be either session or run specific. So far with the help of Adam Thomas and Arshitha Basavaraj we've identified two locations permissible per the validator:

1. As a "comment" row on the `events.tsv` file. Advantage: clearly allowable per spec, relatively free form. Disadvantages: unwieldy for a tabular format to have free-form text, removes ability to attribute a particular note to a particular run.

2. As a metadata entity in the BIDS sidecar .json file. Advantages: straightforward to add in, and in a format that's friendly to free-form text, easy to associate with a particular run. Disadvantage: on a multi-echo dataset, you would have to choose one echo for notes or propagate the notes through all echoes (which would be a pain).

Are there any thoughts on which approach is preferable, or if there is a third approach we haven't considered?

Best,

Josh T.

[Remi Gau]

Will let others chime in but adding those notes in side-car JSON might not be possible in many cases and could throw warnings / error in the validator.

I would suggest the README file for now.

The starter-kit template for README as a section for that at the very end:

https://github.com/bids-standard/bids-starter-kit/blob/master/templates/README

@+

Rémi

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[Kay Robbins]

Joshua,

You could use the HED column of the events.tsv file to annotate the comments. However, the usual way to annotate using HED is to use a single JSON sidecar at the top level of the dataset.

If you do decide to use the HED column of the events.tsv, it does add that column for that dataset. I would recommend that you put the information in the scans file instead as a notes column.

The scans.tsv is much smaller than the events file and so adding a column is not a big deal. Extra columns are permitted in the scans file.

As a side note, we are going to eventually propose adding HED in JSON side cars for scans file so that the scans information can be more easily into analysis without hand coding.  This won't happen for a while though.

I'm not sure that it is currently allowed, but we are planning to propose the addition of columns in the scans file that are described by JSON.

Kay

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From: bids-di...@googlegroups.com <bids-di...@googlegroups.com> on behalf of Remi Gau <remi...@gmail.com>
Sent: Friday, March 12, 2021 8:52 AM
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Subject: [EXTERNAL] Re: [bids-discussion] Placement of experimental notes in BIDS tree

 

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