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# System prepended metadata

title: dMRIPrep Workshop Agenda

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# 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?
1. **Concatenating different `run-`** ([#43]): conclude discussion and get a first implementation merged
    * Revisit/revise [#27].
1. **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](https://github.com/bids-standard/bids-specification/pull/352) to an end
1. **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
1. **SDCFlows** (= susceptibility-derived distortion correction and related issues) - [project](https://github.com/poldracklab/sdcflows)/
    * 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).
1. **Open discussions about Eddy Current Correction (ECC)**
    * to FSL `eddy` or not to `eddy`?
1. **B1 nonuniformity**
    * Extract from sMRIPrep (estimated on the T1w)
    * Can it be applied in the beginning?
1. **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)


[Shared Document]: https://docs.google.com/document/d/1d2oAy5umm9FFoxJVusCJNmIajlYNrBssX182jO-2k1o/edit?usp=sharing
[#24]: https://github.com/nipreps/dmriprep/pull/24
[#25]: https://github.com/nipreps/dmriprep/pull/25
[#26]: https://github.com/nipreps/dmriprep/pull/26
[#27]: https://github.com/nipreps/dmriprep/pull/27
[#43]: https://github.com/nipreps/dmriprep/pull/43
[poldracklab/sdcflows#76]: https://github.com/poldracklab/sdcflows/pull/76
