DSST Lunch & Learn · October 6, 2026

From XNAT MRI and physio to BIDS to visual file analysis

by {{author}}

xnat-bids-cli

​& sqlite-browser

01Broad overviews

TODAY

02Canned xnat-bids-cli demo
03Live sqlite-browser demo
04Questions

“

I have MRI data in XNAT.

I have physio data files.

I want curated BIDS data.

- The xnat-bids-cli use case

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Operations in your control

  • Include & exclude
  • Renaming
  • Quality control
  • Mapping

Tables

Command-line interface:
"Where the magic happens"

  • login
  • query
  • download
  • mriconfig
  • mriconvert
  • physiconvert
  • bidsmap
  • cubids

The CLI part

Uses open source software

XNAT to BIDS

Canneddemos

navigate down
in the slides

A short video of a fresh installation with "pip install"

Installation

A short video of the XNAT query command

query

01

MANUAL STEP 1

Between query & download

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A short video of the XNAT download command

download

02

MANUAL STEP 2

Between download & mriconvert

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A short video of the mriconfig command which runs dcm2bids-helper

mriconfig

A short video of the mriconvert command which runs dcm2bids

mriconvert

03

MANUAL STEP 3

Between mriconvert & physioconvert

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A short video of the physioconvert command which runs phys2bids

physioconvert

04

MANUAL STEP 4

Between physioconvert & bidsmap

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A short video of the bidsmap command used to produce a bidsmap file

bidsmap (part 1)

A short video of the bidsmap command used to map a dataset

bidsmap (part 2)

I made a BIDS!

Now what?

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“

I have lots of BIDS studies.

I want to see what's there.

- The sqlite-browser use case

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bids2table

to the rescue!

Why SQLite?

Why browse?

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A way to:

  • Allow questions to be asked and iterated upon
  • Look at your (meta)data

Browser

Concatenated tables from bids2table:

  • Relational databases
  • Queries can be faster
  • BIDS info is all there

SQLite

Access all the BIDS:

  • File names
  • Entities
  • Sidecar JSONs
  • ... and more!

bids2table

Live demo

navigate down
in the slides
for the setup

A short video of a fresh installation of bids2table and sqlite-browser

Installation

A short video of setting up to run the sqlite-browser app

Setup

01Jen Evans

SPECIAL THANKS

02Dustin Moraczewski
03Catherine Walsh
04All of you! For trying it out, right?
01xnat-bids-cli (docs & GitHub)

RESOURCES

02sqlite-browser* (docs & GitHub)
03bids2table (docs & GitHub)
04These slides (link, asciinema)

* sqlite-browser name subject to change