dMRIPrep Workshop Agenda

Participants

  • Ariel Rokem (organizer, Tel: 5103876264)
  • Anisha Keshavan
  • Adam Richie-Halford
  • Oscar Esteban
  • Garikoitz Lerma-Usabiaga
  • Derek Pilsner
  • Michael Joseph
  • Matthew Cieslak
  • Ross Lawrence
  • (please add your name if not listed)

Tasks

(from the Shared Document)

  1. B0 reference of each run- & brain extraction from that (#25): finalize (if not done before the workshop).
    • Grand mean scaling? (working on this on NiWorkflows right now) - write parameters to correct for signal drift down the line?
  2. Concatenating different run- (#43): conclude discussion and get a first implementation merged
    • Revisit/revise #27.
  3. Data conformity checks (#24):
    • What conformity checks were not addressed by #26?
    • What other conformity checks are needed (e.g., NIfTI x-forms)?
    • Implementation
    • Push Matt's PR to BIDS about b-matrix to an end
  4. Head-motion estimation & reportlet: depending on the design decisions made for #43:
    • implement a head-motion parameters estimation workflow (or reuse from NiWorkflows),
    • rotate b-matrix,
    • generate a reportlet with Anisha's visualization of HMC, and
    • generate FD series for downstream outlier rejection
  5. SDCFlows (= susceptibility-derived distortion correction and related issues) - project/
    • Finalize TOPUP implementation poldracklab/sdcflows#76 - which includes generating the topup/eddy index file.
    • Connect SDCFlows as it is done in fMRIPrep (i.e., enable SDC).
  6. Open discussions about Eddy Current Correction (ECC)
    • to FSL eddy or not to eddy?
  7. B1 nonuniformity
    • Extract from sMRIPrep (estimated on the T1w)
    • Can it be applied in the beginning?
  8. Repository maintenance
    • Unlink nipy/dmriprep
    • Increase code coverage (i.e., write tests for existing code)
    • Start with documentation

Schedule & methodology

Day 1:

​​​​9.00 Touch-base / round table
​​​​  * Driving principles of NiPreps / dMRIPrep (OE)
​​​​  * Open discussions regarding CONTRIBUTING.md, if necessary.
​​​​10.00 Back-to-back groups (two/three people working on one item of those above)
​​​​12.00 Lunch break
​​​​16.00 Individual PR revision
​​​​16.30 Group PR revision

Day 2:

​​​​9.30 Round table
​​​​10.00 Focus: reportlets (OE & MJ)
​​​​  * How to generate them
​​​​  * The report generation factory of NiWorkflows
​​​​10.30 Back-to-back groups (tasks)
​​​​12.00 Lunch break
​​​​13.00 Back-to-back groups (DOCUMENTATION)
​​​​16.00 Individual PR revision
​​​​16.30 Group PR revision

Day 3:

​​​​9.30 Focus: the release process and unit-testing (OE & DP)
​​​​10.30 PR Merge festival and conflict resolution group
​​​​12.00 Lunch break
​​​​13.00 Round table and plans (e.g., plugins)
Select a repo