Agenda for April call | Wed 17 6pm / 5pm / 12noon / 9am

[KirstieJane]

Next dev call: Wednesday 17 April at 6pm CEST / 5pm BST / 12noon EDT / 9am PDT

All welcome, please see BIDS mailing list for zoom link (or ping @KirstieJane!)

Agenda

This agenda is built from the March call (#31) minutes. @KirstieJane has had a little rearrange to hopefull make the meeting flow sensibly 😄

Indexable metadata -- #26

From last month's action list

• Need to add a little more explanation to the indexable_metadata section: Include indexable_metadata in the specification #26 (comment) --- @agahkarakuzu

👉 @agahkarakuzu merged PR #37 🚀 ✨ 💯

• Not yet done - add to ProposedChangesToSpecification.md file 😭
  • @KirstieJane has kinda started in Include symbolic links to derived files #25 (bad git management rather than on purpose) see here but it isn't complete.

Proposed changes to specification -- #41

• Update ProposedChangesToSpecification.md with the changes that @agahkarakuzu made in Insert descriptions into main text #30 --- action @agahkarakuzu

• Key discussion had in the call about why we have justified collecting different scans together under one suffix (eg: MP2RAGE and MPM)

Update examples -- issue #34

• There are a couple of inconsistencies with the examples -- specifically that FLASH is currently used as a suffix --- action @alazari

• MPM examples use a bunch of different suffices:
  • Rename sub-01_echo-1_part-mag_MTw.nii.gz --> sub-01_echo-1_aqc-MTon_part-mag_MPM.nii.gz
  • Rename sub-01_echo-1_part-mag_PDw.nii.gz --> sub-01_echo-1_aqc-MToff_part-mag_MPM.nii.gz
  • Rename sub-01_echo-1_part-mag_T1w.nii.gz --> sub-01_echo-1_aqc-T1w_part-mag_MPM.nii.gz
• Outputs for MPM processing should be in a derivatives folder.

See PR #38

• Comment from @KirstieJane on Created 'derivatives' folder with processed MPM output #38 (comment)
  • Linked PR: Move example RAW data from SOURCE data & add (only one) derivatives pipeline folder lazaral/bep001#1

Symlink - issue #8

• Need to add to the specification something about being able to symlink derivatives files to raw --- @KirstieJane
  • Specifically to allow outputs to be used with current BIDS-Apps.
  • In the future, hopefully the BIDS-Apps will be able to take inputs from the derivatives, so this linking is a band-aid to help qMRI researchers get into the BIDS-App ecosystem, not a long term plan 😄

• Current WIP Include symbolic links to derived files #25 - this is just a bit of a mess because I have too many other files in this branch 😬
  • But if anyone can reveiw what I've written for the common principles section that would be great!

Add examples to specification

• Read through the draft specification looking for where examples can be added to make things clearer --- @tiborauer
  • Useful google doc from @agahkarakuzu: https://docs.google.com/document/d/1HfCjPKCXqTckB0OPs-Py06yY2gPYaFGc0sFTPB74fEA/edit?usp=sharing

Tidy up

• Tidy up the issues and fix a few "little" points --- @Gilles86

Looking forwards

What are the next steps we need to take?

[tiborauer]

Regarding the examples, the current version contains a template
sub-<participant_label>[_ses-<session_label>][_<indexable_metadata>-<index>][_acq-<label>][_part-<mag/phase>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.nii.gz,
so the MPM example should be:

• sub-01_echo-1_acq-MTon_part-mag_MPM.nii.gz
• sub-01_echo-1_acq-MToff_part-mag_MPM.nii.gz
• sub-01_echo-1_acq-T1w_part-mag_MPM.nii.gz
  (i.e. "acq" before "part")

[KirstieJane]

Hey @tiborauer - would you mind opening a new issue? I can link to it in the agenda. This thread might get rather overwhelmed if we all comment here....

[KirstieJane]

Oh wait - sorry - it's my text that's wrong.... I'll fix that.

(update, fixed!)

[tiborauer]

Done! See #34

[Gilles86]

Let's also talk about a possible OHBM meeting in Rome.

[Gilles86]

We need to talk about where B1 fieldmap should go and what their filename should look like.

[KirstieJane]

Hey folks - I'm taking minutes here - come and join me 😉
https://hackmd.io/MRTYVroETa2aKvwVjNaKGg

[KirstieJane]

Closing as I hope I've captured all the points in #47