This is a datman/dashboard-ized version of Jer's lovely niviz-rater app.

Installation

1. install the dashboard if you haven't already. Note that the below instructions are for users following the 'full installation' instructions.
2. Add datman_niviz to the blueprint folder

cd datman-dashboard/dashboard/blueprints
git clone [email protected]:TIGRLab/datman_niviz.git

3. Install the requirements

pip install -r datman_niviz/niviz_rater/requirements.txt

4. Build the static files. Note that you must have npm installed. If this step is successful it will have created the folder datman-dashboard/dashboard/static/niviz_rater.

cd niviz_rater/static_src
npm install
npm run build

5. Configure your shell's paths. Update the PYTHONPATH.

export PYTHONPATH=${your_dash_install_path}/dashboard/blueprints/datman_niviz:${PYTHONPATH}

Update the PATH.

export PATH=${your_dash_install_path}/dashboard/blueprints/datman_niviz/niviz_rater/bin:${PATH}

6. Provide the full path to the configuration file in the NIVIZ_RATER_CONF environment variable. See the 'Configuration file' section for more info.

export NIVIZ_RATER_CONF=$your_config_file_path

7. Initialize the databases. You must run this as the user that the dashboard will use to access the database.

init_db.py

Configuration File

For the dashboard to host niviz-rater, a configuration file must be provided using an environment variable named NIVIZ_RATER_CONF. This file must be yaml format and must contain one entry per pipeline.

Each entry must be formatted like below:

STUDY_pipeline:
  base_dir: /some/path/to/niviz_rater/data
  qc_spec: /some/path/to/niviz_rater/spec_file.yaml
  bids_config: /some/path/to/alt_config.json          # bids_config is optional
  schema: /some/path/to/alt/schema.yaml               # schema is optional

STUDY_pipeline is the name to use when accessing the data through niviz-rater, and the name that will be used for the database.

• 'STUDY' must be the name of a datman managed study.
• 'pipeline' must be a unique name for the pipeline data to be displayed by niviz-rater. Note that this field MAY contain underscores, but otherwise must consist only of alphanumeric characters (e.g. using '-' or a blank space in a pipeline name will cause issues.)
• Note that 'STUDY' and 'pipeline' MUST be separated by an underscore.

At a minimum you must specify the base_dir and qc_spec arguments for each entry. Any additional options you wish to pass to niviz-rater may be included.