The command line

The commands

Command	What it does	In the GUI
`bidsmgr`	Opens the GUI
`bidsmgr-create`	Creates a project	Home > Create a new dataset
`bidsmgr-adopt`	Makes an existing BIDS dataset a project	Home > Open dataset folder
`bidsmgr-project`	Lists a project's scan tables	Scan table, in the Converter
`bidsmgr-scan`	Scans raw data into a scan table (`inventory.tsv`)	Scan…
`bidsmgr-classify`	Names MRI series again from their acquisition parameters	Settings > Classification
`bidsmgr-rebuild`	Rebuilds the BIDS names of an edited `inventory.tsv`	Editing the table
`bidsmgr-convert`	Converts a scan table	Run conversion
`bidsmgr-metadata`	Writes the dataset's metadata and TODO placeholders	the post-convert chain
`bidsmgr-validate`	Validates a dataset	Validate dataset
`bidsmgr-deface`	Removes faces, or keeps the brain only	Tools > Deface
`bidsmgr-qc`	Runs the quality check	Tools > Quality check
`bidsmgr-view`	Opens an image in the viewer, or renders it to a file	the viewer

--help on any of them lists its options; every option is in Command line.

Convert the course's project

The project keeps the scan table and every edit you made to it in the GUI, so the commands can pick up where the GUI left off. --project names the project folder.

Step 1. List the project's scan tables

Terminal

$ bidsmgr-project /tmp/studies/multimodal_study
Project: /tmp/studies/multimodal_study
  1 scan version(s); active = latest:
  * 0001__raw  [curating]  19 rows  source=raw  raw=/tmp/studies/BIDS_Manager_multimodal_sample_v2/raw

The table marked * is the one the other commands use, unless --version names another.

Step 2. Convert it

Terminal

$ bidsmgr-convert --project /tmp/studies/multimodal_study -j 4

The conversion replays the edits recorded in the project (one subject, one session, the spectroscopy names) and the PET dose values saved with the scan table. The description and the participants file are written by the next step, bidsmgr-metadata. -j 4 converts four series at a time. It took 5.3 seconds on the sample.

Step 3. Write the metadata

Terminal

$ bidsmgr-metadata --project /tmp/studies/multimodal_study --fill-todos
  TODO placeholders inserted: 69 fields across 8 files

--fill-todos writes the TODO placeholders the GUI's default post-convert chain writes; --fill-scope required|recommended|optional chooses how far they go.

Step 4. Validate

Terminal

$ bidsmgr-validate /tmp/studies/multimodal_study --strict --html
=== /tmp/studies/multimodal_study ===
  severity: ERR  (ok=27 warn=112 err=1)

--strict runs the deep checks and --html writes validation_report.html into the project's .bidsmgr/ folder. The result is the GUI's, file for file: the same 65 files, the same one error (chapter 9 fixes it).

From raw data to BIDS in a script

For a study you convert the same way every time, the whole workflow can run without the GUI:

Terminal

$ bidsmgr-create /data/bids/my_study --name "My study"
$ bidsmgr-scan /data/raw/my_study --project /data/bids/my_study -j 8
$ bidsmgr-convert --project /data/bids/my_study -j 8 --pet-spreadsheet dose_sheet.csv
$ bidsmgr-metadata --project /data/bids/my_study --participants participants.csv --fill-todos
$ bidsmgr-validate /data/bids/my_study --strict --html

What the GUI lets you do between the scan and the conversion (reconcile subjects, rename a task, leave a series out), a script does in inventory.tsv. Two ways:

Scan rules in a JSON file (bidsmgr-scan --rules-file rules.json): leave out series by name and give your own names to series, applied at every scan. Settings > Scan rules keeps rules of the same form in BIDS Manager's own settings, but cannot save them to a file; write the JSON by hand (bidsmgr-scan --help shows its form).
Edit inventory.tsv, a tab-separated table, then run bidsmgr-rebuild to rebuild the names. The entities column holds every row's entities as JSON and is what the names are built from: edit it, and run bidsmgr-rebuild inventory.tsv (the default, --from entities).

Without a project

The commands also work on a free-standing inventory.tsv and output folder, which suits one-off conversions:

Terminal

$ bidsmgr-scan /data/raw/my_study inventory.tsv -j 8
$ bidsmgr-convert inventory.tsv /data/bids --raw-root /data/raw/my_study -j 8
$ bidsmgr-metadata /data/bids/my_study --fill-todos
$ bidsmgr-validate /data/bids/my_study

The dataset folder is named after the raw folder (in lower case) unless bidsmgr-scan --dataset names it. Without a project, nothing records your edits and there are no scan versions; for anything you will come back to, use a project.

Viewing and checking from the command line

Terminal

$ bidsmgr-view sub-001/ses-01/anat/sub-001_ses-01_acq-tfl3p2_T1w.nii.gz --layout multi
$ bidsmgr-view T1w.nii.gz --render t1.png --planes axial coronal --height 400
$ bidsmgr-qc /tmp/studies/multimodal_study --datatype anat dwi -j 4

--render draws the image to a file without opening a window, which works on a server. Save > Show the command line... in the viewer writes the bidsmgr-view command that reproduces what is on screen.