Douglas node with 2 datasets and connection to us

[surchs]

Context

The Douglas has had a deployed neurobagel node since https://github.com/neurobagel/project/issues/105. From this we got a lot of valuable technical feedback. But the node isn't very useful to the Douglas yet, and as a result we do not yet get any valuable user feedback. So the goal is to change this and then keep going.

Why

• Part of Grow the amount and usefulness of data #11 and Grow userbase #49
• So the Douglas / Cobralab gets value out of neurobagel
• So we get hands on feedback from target users on what they like / need from query
• To have a concrete example to show Douglas stakeholders when discussing expansion

Outcomes

• minimum PEPP in the Douglas node
• PNC in the Douglas node
• raw NIfTi BIDS versions of PEPP and PNC converted to MNC
• Douglas node has read-only federation with the public neurobagel network (i.e. they see all that query.neurobagel.org sees)

What

• document how to run F-API locally documentation#129
• https://github.com/DouglasNeuroInformatics/project_issues/issues/70
• https://github.com/DouglasNeuroInformatics/project_issues/issues/69
• (re-) BIDSify PEPP and PNC on DNP storage (Matt or NB)
• (re-) annotate PEPP data (Matt or NB)
• [ ] annotate PNC data (Matt or NB)
• process annotated datasets with CLI to create graph ready files (Matt or NB)
• ingest graph data into node (Gabe or Thomas)
• [ ] clarify process to keep Douglas node in sync with files on disk
• Deploy FRP on our machine #127
• Configure and demonstrate MNI - Douglas federation #128
• Confirm federation from DNP to MNI

TBD / maybe later

• train Cobra lab members to annotate PEPP + PNC
• run MNC conversion on the BIDSified data
• clarify choice of NIfTi to MNC converter with Gabe

[gdevenyi]

run MNC conversion on the BIDSified data

Until a tool is produced which can use BIDS + the native metadata in dcm2mnc produced MINC files to rename/organize into MINCBIDS type format, we were just do conversion "as needed"

clarify choice of NIfTi to MNC converter with Gabe

nii2mnc from the latest minc-toolkit-v2 release