---
# System prepended metadata

title: 'HBN Preprocessing Meeting #1'

---

# HBN Preprocessing Meeting #1

## Attendees (alphabetical by last name)

- Matt Cieslak (Penn BBL)
- Alexandre Franco (CMI)
- John Kruper (NRDG/UW)
- Mike Milham (CMI)
- Adam Richie-Halford (NRDG/UW)
- Ariel Rokem (NRDG/UW)
- Ethan Roy (NRDG/Stanford)
- Ted Satterthwaite (Penn BBL)
- Valerie Sydnor (Penn BBL)
- Jason Yeatman (NRDG/Stanford)

## Minutes

0. Study Scope
    - There was some discussion about whether or not to include Site-SI and Site-CUNY. We agreed to include every site and annotate differences.
    - In particular, some subjects from Site-CBIC were scanned using the ABCD protocol. This should be noted.
    - We will include Site-SI, but also note the potential harmonization issues.
    - There are some participants in the FCP-INDI S3 bucket that are not listed in `participants.tsv` files. Adam will send a list of these participants to Alex and Alex will remedy.
    - Penn BBL has put considerable amount of work into curating the HBN data for Site-RU and Site-CBIC. Ted will work with Alex to put that on FCP-INDI S3. They also have a todo item to repeat this curation with Site-SI and Site-CUNY, however, the timeframe for this is unknown.
0. Preprocessing parameters
    - Matt will send out an example html report with all of the preprocessing parameters
    - eddy linear vs quadratic discussion: quadratic is the eddy default so it's what most other groups do. Matt set linear as the default in qsiprep. We agreed to do a comparison of linear vs quadratic in a sample that overlaps with the already processed Site-RU subjects, excluding obliques. 
    - We agreed on 1.8mm isotropic output resolution for all subjects
    - For Site-CBIC, we will use VNAV T1w
    
0. Prerequisite qsiprep enhancements
    - Oblique scans
        => Fixed in an upcoming qsiprep release
    - Desired additional output report components
        => Ribbons of WM/GM on the registration plots
    - Matt and Adam are also working on dmriprep-viewer which will help with visualization of output. It should be possible to generate the required json reports for this tool using the `--reports-only` flag for qsiprep. This way we can start the preprocessing without waiting on dmriprep-viewer development.
0. QA protocol
    - QA team members (so far):
        - Adam Richie-Halford
        - Ariel Rokem
        - Valerie Sydnor
    - The following qsiprep output will be useful for QA at the group level:
        - Neighboring DWI correlation
        - Changes in FWHM compared to Raw data
        - Eddy CNR average
        - T1w dice coefficient
        - Head motion mean/max
    - We decided to use Braindr for QA of all subjects, with five slices per volume and the following images as input:
        - b=0 reference image
        - eddy CNR
0. Computation
    - Ariel volunteered the NRDG group to do the preprocessing using AWS resources. This may cost as much as $1.00 per subject. Everyone agreed.
0. Open dataset
    - We agreed to store the generated data on FCP-INDI S3:
        - Curated input data
        - qsiprep container
        - qsiprep output in derivatives directory
    - We decided not to put the qsiprep working directory files on S3
    - Alex will ask Mike about granting write access to FCP-INDI S3 to Ariel and Adam so that they can directly upload qsiprep results.
0. Publication
    - Sections:
        - the HBN dataset
        - the need for standardized preprocessing
        - qsiprep
        - preprocessing at scale, challenges and solutions
        - BrainDr / QC
        - visualization section (e.g. dmriprep-viewer)
    - Who is doing the work:
        - Ariel and Adam agreed to spearhead the project and paper
        - We will benefit greatly from the data curation work already completed by Penn BBL and from the development of qsiprep.
0. When to meet again
    - We agreed to meet again after Site-RU and Site-CBIC have been preprocessed. We will discuss:
        - BrainDr
        - Any issues with Site-SI and Site-CUNY
        - dmriprep-viewer
    - Given the estimated due dates for the tasks below, this meeting will be after 04 Sep 2020.

## Action Items

| Todo | Assignee | Due By |
| :- | :- | :- |
| ~~Compile Todo items and send to attendees~~ | Adam Richie-Halford | 11 Aug 2020 |
| Send list of subjects not in `participants.tsv` to Alex | Adam Richie-Halford | 12 Aug 2020 |
| Update participants.tsv to include the aforesaid subjects | Alex Franco | 21 Aug 2020 |
| Upload curated data for Site-RU and Site-CBIC to FCP-INDI S3 | Ted Satterthwaite | 17 Aug 2020 |
| Repeat curation for Site-SI and Site-CUNY, upload to FCP-INDI S3 | Ted Satterthwaite | 04 Sep 2020 |
| Confirm that the curated data json sidecars for Site-CBIC will make qsiprep use the VNAV T1w | Ted Satterthwaite | 17 Aug 2020
| Send out example html report with all of the preprocessing parameters | Matt Cieslak | 14 Aug 2020 |
| Work on dmriprep-viewer | Adam Richie-Halford and Matt Cieslak | Ongoing |
| Add ribbons of WM/GM on registration plots to output reports (either in the output html or in dmriprep-viewer) | Matt Cieslak and Adam Richie-Halford | 28 Aug 2020 |
| Ask Mike about granting Ariel and Adam write access to FCP-INDI S3 bucket | Alex Franco | 14 Aug 2020 |
| Once curated data is on S3 and FCP-INDI S3 write access is obtained, run qsiprep on all subjects in Site-RU and Site-CBIC. Reconfirm qsiprep params before production run | Adam Richie-Halford | 04 Sep 2020 |
| Do it again for Site-SI and Site-CUNY | Adam Richie-Halford | 11 Sep 2020 |
| Set up braindr | Adam Richie-Halford and Ariel Rokem | 18 Sep 2020 |


