Files BIDS Manager writes

The dataset

File or folder	Written by	What it is
`dataset_description.json`	creating the project; the conversion; the metadata step	The dataset's name, BIDS version, authors, licence, and what generated it.
`README`, `CHANGES`	creating the project (README); the metadata step (both)	A starting README to replace with a description of the dataset, and a change log.
`.bidsignore`	creating the project	Tells validators to ignore `.bidsmgr/` and the conversion's scratch folder.
`participants.tsv`, `participants.json`	the metadata step	One row per subject, and the description of each column.
`sub-<label>/[ses-<label>/]<datatype>/`	the conversion	The recordings, each with its sidecar and companion files.
`sub-<label>/[ses-<label>/]sub-<label>[_ses-<label>]_scans.tsv`	the metadata step	Each recording of the session with its acquisition time.
`task-<label>_bold.json` and other sidecars at the top	Tools > Fix ups... > Move shared fields up	Sidecars shared by many files (inheritance).
`phenotype/`	the metadata step, with a phenotype spreadsheet	Questionnaires and measures, one table per instrument.
`CITATION.cff`	Tools > Fix ups...; `bidsmgr-metadata --write-citation`; the post-conversion setting	How to cite the dataset, from its description. Optional.
`sourcedata/`	the conversion, when Keep in sourcedata/ is on	The raw files of each subject, as they were or as one archive per series, with a `manifest.tsv` of checksums.
`derivatives/bidsmgr-qc/`	the quality check	Its results, per image, so they are not computed twice.
`derivatives/bidsmgr-skullstrip/`	Tools > Remove the skull...	Skull-stripped images, as a derivative dataset.

The .bidsmgr folder

BIDS Manager's own folder in the dataset. It is listed in .bidsignore, so validators skip it, and it is what makes scans resumable and every change traceable. Leave it out when you share the dataset (Sharing a dataset).

.bidsmgr/
├── project/
│   ├── meta.json                  the project: name, BIDS Manager and BIDS versions, creation time
│   ├── events.jsonl               what happened to the project, one event per line
│   └── scans/
│       └── 0001__raw/             one scan table
│           ├── inventory.tsv      the scan table, as last saved
│           ├── inventory.tsv.recording_meta.json   the dataset metadata you gave
│           ├── events.jsonl       every edit made to this table, for Undo
│           ├── version.json       where the raw data was, and the table's state
│           └── ...                the scan's caches (series files, features)
├── editor/
│   ├── operations.log             every change made in the Editor, one per line
│   └── originals/                 the files as they were before each change
├── logs/                          one log per scan, conversion, metadata step and validation
├── provenance/                    per subject: what the conversion did, with which tools
├── errors/                        per subject, when its conversion failed: the reason
├── backup/                        files an update conversion replaced
├── merged/<source>/               the history of a subject merged into another
├── adopted_manifest.json          for an adopted dataset: every file as it was found
├── accepted_findings.json         validation findings you accepted
├── viz/scenes/                    viewer scenes you saved
├── metadata_report.json           what the metadata step filled, and every TODO it wrote
├── validation_report.json         the last validation's findings
└── validation_report.html         the same, as a page to read or send

During a conversion each subject is written into .tmp_bidsmgr/sub-<label>/ in the dataset first, and moved into place only when it converted completely. The folder is removed afterwards; if you find one, a conversion was interrupted, and it can be deleted.

Outside the dataset

What	Where
Your settings and recent projects	your user account (First launch)
Logs of commands run outside a project	`~/.bidsmgr/logs/`
A scan without a project	the scan table file you name, with its caches beside it (`inventory.tsv.files_by_uid.json.gz` and similar)

BIDS Manager writes nothing into the raw folder you scan.