Setup

config sets where NeuroAtlas reads datasets and writes caches, results and model weights. Configuration explains the settings.

config

Set where NeuroAtlas reads datasets and writes caches, results and model weights. The settings are saved in ~/.neuroatlas/config.yaml, or in $NEUROATLAS_HOME/config.yaml when that variable is set.

Usage: neuroatlas config <action>

Command	Description
config init	Write the settings file.
config show	Print each setting, whether its folder exists and where the value comes from.
config set	Change one setting.
config unset	Remove one setting, so it goes back to its default.
config path	Print the path of the settings file.
config token	Save a Hugging Face, GitHub or NSRR token.

config init

Write the settings file. With a project folder DIR, everything goes to DIR/data, DIR/cache, DIR/results and DIR/models. A --*-root option moves one of them.

Usage: neuroatlas config init [DIR] [options]

neuroatlas config init ~/neuroatlas
neuroatlas config init ~/neuroatlas --data-root /data/eeg    # datasets elsewhere

Option	Description	Default
DIR	Project folder. Its sub-folders are created when needed.
--data-root DIR	Folder with the raw datasets, one sub-folder per dataset.	DIR/data
--cache-root DIR	Folder for saved embeddings and prepared datasets, which can grow large.	DIR/cache, else $NEUROATLAS_HOME/artifacts/embedding_cache
--output-root DIR	Folder for the probe results.	DIR/results, else $NEUROATLAS_HOME/artifacts/benchmarks
--models-root DIR	Folder for model weights.	DIR/models, else $NEUROATLAS_HOME/artifacts/models
--dataset-path DATASET.KEY=PATH	Folder of a dataset kept elsewhere, as in ucddb.data_root=/mnt/ucddb. Can be repeated.
--force	Overwrite an existing settings file.

config show

Print each setting, whether its folder exists and where the value comes from.

Usage: neuroatlas config show

neuroatlas config show

config set

Change one setting. KEY is data_root, cache_root, output_root, models_root or a dataset folder such as chbmit.bids_root. neuroatlas data status DATASET shows the key a dataset reads.

Usage: neuroatlas config set key value

neuroatlas config set ucddb.data_root /mnt/ucddb
neuroatlas config set cache_root /scratch/neuroatlas_cache

Option	Description	Default
key	Setting name, such as data_root or ucddb.data_root.
value	New value, usually a folder.

config unset

Remove one setting, so it goes back to its default.

Usage: neuroatlas config unset key

neuroatlas config unset ucddb.data_root

Option	Description	Default
key	Setting name.

config path

Print the path of the settings file.

Usage: neuroatlas config path

neuroatlas config path

config token

Save an access token for Hugging Face (hf), GitHub (github) or NSRR (nsrr). Type it when asked, or pipe it in as in neuroatlas config token hf < file. It is saved to $NEUROATLAS_HOME/<name>_token, readable only by you, and never printed.

Usage: neuroatlas config token {github,hf,nsrr} [options]

neuroatlas config token nsrr
neuroatlas config token hf --remove

Option	Description	Default
{github,hf,nsrr}	hf for gated Hugging Face repositories, github when GitHub refuses a download, or nsrr for the NSRR sleep datasets.
--remove	Delete the saved token.