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Given that pre-reg now falls the more under "unspecified" aspect of data description, I suspect it could at least have an entry in the FAQ of the starter kit.

bids-standard/bids-specification#572

@emdupre mentioned this in #56 (comment), which was followed up by @effigies and @adelavega

I had a go at it and implemented a menu using bootstrap, which is now part of the deployed website. However, my html/css/js skills are not that great. Could you please check that it renders properly on your devices and/or in your browser?

If you have suggestions to improve the rendering of the header+menu, please suggest them as a PR.

https://github.com/INCF/bids-starter-kit

Currently the website does not have drop down menus to the tabs enabled. Having these drop-down menus can ease users attempting to navigate to specific locations on the website. Extensibility can be built in to extend these tabs as we run into more use cases. I think this will assist in extracting specific information from the website.

We can use this issue to identify and document the tabs we would like to add.

Adding to:

• Getting started: adding tutorials, starter kit

The feedback on neurostars included multiple people suggesting to move away from thewhite-on-black, and @emdupre specifically mentioned accessibility at https://neurostars.org/t/request-for-feedback-reorganizing-bids-website/5476/3

For me personally a11y was a new term, but I figured it out by now.

as mentioned by @yarikoptic in #56 (comment) and by @sappelhoff

I have made local changes to index.html, but I do not seem to have permission to submit a pull request though I am logged in to github:
Uploads are disabled.
File uploads require push access to this repository.

Here are the changes:
index.html.gz.

Description of changes: I added a link to the 2017 paper and I reorganized the list of apps so the bids-apps page is at the top, and then apps are organized alphabetically into nested categories.

However, I have to wonder why some apps are listed here and then a partially overlapping list is on the bids-apps page. It seems like you are doubling your work to maintain 2 lists.

With the constantly growing number of resources about BIDS, I thought it would be useful to organise the "flow" that we expect newcomers to follow -- starting from Googling "what is BIDS" to finding their answer.

This is just a rough skeleton so far, but happy to hear any input related to this!

@gllmflndn mentioned that this information is "a bit" hidden and could maybe benefit from being more visible on the website itself.

In the governance page?

I think the tutorials can be directly linked to our website rather than adding the additional clicks and platform change to the process. (this may help with our search indexing?? - there has been trouble locating tutorials)

The tutorials of interest are located on our starter kit

This may be seen as duplicating but this is a crucial part of the BIDS process and moves toward a robust system of support.

To be honest, I've already done this based on general consensus (from a small number of people) in #56 which implements a new website.

I figured I'd make an issue and close it just so we have a paper trail of who did what and why!

@robertoostenveld is a member of the BIDS steering group and long term contributor to the standard. He's made a new version of the website and it makes sense that he has some ability to fix bugs quickly as they appear.

Shout if you disagree with my action.

We're already hitting a few crossed wires with folks working on the same topic at the same time. Hopefully we can smooth that out in the long run, but for now I think we should definitely protect the master branch to require at least 1 review before PRs are merged.

What do folks think? What would be reasonable?

At the bottom of https://bids.neuroimaging.io/ the link to the INCF is incorrect. Also the link on the INCF site for the task force has been moved/removed.

The Feedback link at the top of the page sends you to the bottom of the page but there's nothing there about giving feedback...

If #56 gets merged, there is some technical follow up work to be done:

• re-enable google analytics
• consider whether PDF with previous versions of the specification should remain hosted on the website
• get a pdf version of the 2016 poster (the svg version is broken)
• ensure that the contributing guidelines and code of conduct still work on github

Related to ongoing discussion in #76, it would be good to enable PR-associated builds to simplify reviews.

The approach used in bids-standard/bids-specification#315 seems pretty straightforward. As an organization owner, I will go ahead and enable CircleCI and the artifacts redirector on this repository. If somebody has the time and inclination to put together a CircleCI config, please comment and let us know.

If nobody has time before then, I should have some on Monday.

This isn't to short-circuit discussion about netlify or other options. I vaguely remember not finding it easy to get netlify going, but I can't remember why.

I also recently saw nipreps/dmriprep#52, which suggests that perhaps there's a way to use GitHub actions to build docs on PRs. It hasn't been merged, so I don't know how viewing them would look.

at least one link on https://bids.neuroimaging.io/governance.html is broken --> https://predictablynoisy.com/rust-governance

Right now the menu item links to a page that subsequently links to the specification.

This was suggested by @CPernet in #56 (comment) and later also by @jbteves.

However, @adelavega argued against it in #56 (comment).

Source https://docs.google.com/document/d/1pWmEEY-1-WuwBPNy5tDAxVJYQ9Een4hZJM06tQZg8X4/edit?disco=AAAABQ0U5J8&ts=59dba09b

In light of discussion where starter kit might get overhauled, having a redirect might give us flexibility to move it in the future without breaking old versions of the spec.

We could use https://bids.neuroimaging.io/starter-kit

The Steering Group has requested for community feedback an idea to organize the bids website. The proposal and conversation can be found on NeuroStars

@chrisfilo I collected some feedback regarding BIDS. I am posting it here near verbatim:

Oh. I just remembered my biggest problem with BIDS.
BIDS and the BIDS validator work great for single session studies or completed studies. I am having major issues using it for longitudinal studies.
If you use it for single session studies then you can run the bids validator after you add a scan. This works great. You can see if you are missing any data or if there are problems with your protocol that doesn’t match the other scans.
If you do the same thing for a longitudinal study then the as soon as you scan the the second session the other subjects that have a single session will be reported as missing the second session. The output can be very extensive and hide valuable information from the second scan.
I haven’t found a good way of dealing with this. I have modified the .bidsignore file to ignore the first session scans (or a portion of them) but I also have to modify the participant.list
This is straightforward to do but I have made mistakes and have had to go back and recreate the file.
It would be nice to have a flag in the bids validator to ignore sessions that have not been acquired yet from the output.

Additional Feedback:

We use the heudiconv converter. It works great and puts things into BIDS format.
My biggest complaint is the data structure is fine but there are many missing modalities that are still missing (Arterial Spin Labeling, Susceptibility Weighted Imaging, and Magnetization transfer). ASL and SWI have been proposed as enhancements but have not been accepted yet. This is a minor inconvenience. I use the .bidsignore file to eliminate these from the bids validation.

For links that point to an offsite page (such as BIDS extension proposals on Google Docs), it would be nice for these to open into a new tab using target=”_blank”. otherwise the reader loses the context for the new page.

Both are now in a decent state for the community to work on, with a github issue and a google doc. See

• bids-standard/bids-specification#438
• bids-standard/bids-specification#443

@sappelhoff do you know whether a specific procedure applies, or do I just assign them a number and add them here to the website?

related to enabling circle CI on this repo (#81) we can think about adding consistent styling similar to what we enforce in the bids specification repository.

similar to the specification this will ensure consistency within (and across) our repositories

I propose that we disable the wiki for this repository. Do you agree @dorahermes ?

the website builds with CircleCI seem to be broken in two ways:

1. the artifact redirect github action does not work
2. when manually getting the artifact from CircleCI, the formatting of the website seems broken

This can be checked with all currently open PRs. E.g., #104

This feature was originally introduced after #81.

edit: another note --> the rendering of the website was apparently fixed by adding the --baseurl option to the jekyll build, see d5ce5af

Hi dear BIDS team,
wouldn't it make sense to change the participants.tsv to standardize for multiple sessions:

• add a column for session-id
• add a column for AcquisitionDate and PatientBirthDate, PatientSex and PatientWeight from the dicom header.
• calculate age from that information

Best,
Niklas

It seems that most of our BEP process is either stored in google docs, or on the wiki of some of the repos.

https://github.com/bids-standard/bids-specification/wiki

I suspect some of the important but implicit details of the process are also stored in the grey matter of several of the maintainers + steering committee. 😄

This kinda makes it hard for outsiders to see and understand how they should go about contributing to BIDS when it comes to BEP.

I suggest we try to centralize most of that information into a single page on the website and add a very obvious link to this on the landing page.

This was suggested by @choldgraf in https://twitter.com/choldgraf/status/1198737801107271680

As discussed in the steering group, we want to post a news item that introduces us. @KirstieJane has been working on a draft.

I will do some work on the technical side to allow news items to appear with a time-stamp, in reverse chronological order, with an author, with an excerpt and a link to a full page, etc.

(related to #93 )

Here are some suggestions for minor changes to top level menus:

ABOUT
NEWS
BENEFITS
SPECIFICATION
GET STARTED
GET INVOLVED
SOFTWARE
GOVERNANCE
ACKNOWLEDGMENTS

• Here THE SPECIFICATION becomes SPECIFICATION to make it shorter.

• GETTING STARTED becomes GET STARTED to make shorter and parallel to GET INVOLVED.

• SOFTWARE (or maybe TOOLS?) is added because right now a list of SOFTWARE using BIDS is under the BENEFITS page which is not where I would look. Having its own menu item promotes software and/or tools, which most BIDS users are going to be particularly interested in.

• Also, could the GET_INVOLVED page benefit from the addition of a brief statement about how to get tools listed or contributing BIDS apps?

Hi developers,

We are using the BIDS format to convert and analyze all our data, and are very much looking forward to the extensions for EEG, PET, etc.

There is a problem we have encountered though. After converting and analyzing MPRAGE data, we are now turning to fMRI and DTI. Turns out that some subjects have sessions with fMRI data without MPRAGE data, and these fall between existing sessions in our analyzed MPRAGE data (i.e., between sess-01 and sess-02). What is the approach for integrating an intermediate session between existing sessions? Is this something BIDS is naturally designed for, or is this a problem to face each time a session falls in time between existing sessions.

Dorian

right now, if one navigates to the site it is not obvious where the extensions are found. I propose adding a top-level heading for extensions, separate from the "getting involved" page.

@KirstieJane posted the "Meet the BIDS Steering Group" item. To facilitate dissemination, it should be possible to directly link to this, and have it rendered as separate page (including photo's).

Going over all BEPs, I noticed in some of them (i.e. in the google docs) that they have been merged with another BEP (mainly with BEP003) and therefore not active any more.

Once #77 is merged, I propose we update the list of BEPs and move the ones that are not actively being worked on to the bottom of the list (along with MEG, EEG, etc)

e.g. bids-matlab should be mentioned, as suggested by @CPernet in #56 (comment)

At the moment, we can link to specific news items by adding the heading in lower case (and with - instead of spaces) but it isn't easy to get that link itself.

For example:

• https://bids.neuroimaging.io/news.html#meet-the-bids-steering-group
• https://bids.neuroimaging.io/news.html#new-website
• https://bids.neuroimaging.io/news.html#bids-steering-group-election-and-governance-results

Does anyone know of any css etc that can make it easy to get the link - for example by hovering over the heading itself?

With all terms accessible via URL.

For each release (but not the draft - too hard to sync).

Suggested by @mih.

As part of the website (general code of conduct for all BIDS related activities) and CODE_OF_CONDUCT.md

Example: https://github.com/WhitakerLab/BrainsForPublication/blob/master/CODE_OF_CONDUCT.md

I can volunteer to be listed as contact person Chris Gorgolewski [email protected]

Earlier in January, the Steering Group hosted 2 virtual community forums. These community forums were recorded and later published on youtube (first and second session).

These videos may be embedded into the community forum blog post to ease the rewatching of these forums by the community.

Dear BIDS team,

First of all, thank you for this great data structure, I have been using this guideline to handle all the data, and have been developed several tools that utilizing BIDS and it is became amazingly efficient.

I'm opening this issue because I hope to ask adding my BIDS compatible converter for preclinical MRI (Bruker raw data). If this is not the place to request this, please let me know, I will close this issue as soon as possible.

Briefly, my code is designed to help to convert multiple sets of raw data for the Bruker's preclinical scanner by creating an excel file and JSON file as a template to guide filename as well as metadata parsing with custom syntax. So I think this will be a useful tool for the animal MR imaging researcher who wants to adapt BIDS for their research.

Here is my Github link : BrkRaw
And below content is what I posted at README.md regarding the BIDS.

Automatic BIDS organizer with template files

The usage of the command-line tool 'brkraw' for BIDS data organization.

• Upgraded feature to reduce the burden on renaming according to BIDS standard.
• Create a BIDS file table with excel format to use as a template for updating metadata that required to use for file naming.
• This command will also generate the BIDS_META_REF.json which allows you to set custom syntax to parse the metadata from the raw data. The default reference of the current version is based on BIDS 1.2.2.
• To learn more detail, please check our example
  Jupyter Notebooks.

$ brkraw bids_list <parent folder> <filname>.xlsx

• Build BIDS dataset according to the excel file generated with 'bids_list' command above.

$ brkraw bids_converter <parent folder> <BIDS table file.xlsx>

$ brkraw bids_converter <parent folder> <BIDS table file.xlsx> -r <BIDS meta reference file.json>

Again please let me know if I post this at the wrong place.
Thank you! and I hope you are all staying safe and healthy from COVID-19!

We recently introduced CircleCI to this repo to build the website upon each PR and provide a link to inspect the result.

Unfortunately, the links on the site do not work, because a .html is missing from each link except the initial link to the main site (index.html)

See https://19-38337026-gh.circle-artifacts.com/0/home/circleci/project/_site/index.html

and try clicking on (e.g.) the "get involved" link, which will direct you to:

https://19-38337026-gh.circle-artifacts.com/0/home/circleci/project/_site/get_involved

this URL is not working unless you append .html

Using the most recent Firefox browser, several links on bids.neuroimaging.io do not work as expected. Nothing happens when clicked upon - only through right-click "open in new tab", the links do work.

This is True for e.g.,

... but also for

(Which are arguably the two most important links?)

Lastly, one would expect that http://bids.neuroimaging.io/bids_spec.pdf would link to the most recent BIDS version, which at this point it does not.

Describe how one can contribute to this repository (the bids.neuroimaging.io website)

https://opensource.guide/how-to-contribute/#how-to-submit-a-contribution
https://github.com/emdupre/me-ica/blob/py3/CONTRIBUTING.md

Hi!

Is it possible to switch to light background colour and a bit bigger fontsize for the text?
I find it a bit hard to read. What do you think?

Thanks!

Currently links to outdated Google Doc. Should point to PR and/or rendered draft.

Can probably do this tomorrow if nobody is feeling itchy and needs something to do. :-)

Related to #96.

it would be useful if there was a way to resolve individual BEPs to their appropriate page (be it on google docs or wherever). e.g.:

https://bids.neuroimaging.io/BEP003 which would resolve to <google doc>

I'm not sure if github pages has a way to do this but it would be nice to have a more permanent identifier for each BEP.