The Neurobagel Query Tool
Neurobagel's query tool is a web interface for searching across a Neurobagel graph based on various subject clinical-demographic and imaging parameters.
The query tool is a React application, developed in TypeScript using a variety of tools including Vite, Cypress, and MUI.
Quickstart
The query tool is hosted at https://query.neurobagel.org/ and interfaces with Neurobagel federation API.
Local Installation
To run the query tool locally, you have two options:
- Use our docker image
- Do a manual install from the cloned git repo.
but before proceeding with either you need to set the environment variables.
Mandatory configuration
| Environment variable | Type | Required | Default value if not set | Example |
|---|---|---|---|---|
NB_API_QUERY_URL |
string | Yes | - | https://federate.neurobagel.org/ |
NB_QUERY_APP_BASE_PATH |
string | No | / |
/query/ |
NB_ENABLE_AUTH |
boolean | No | false |
false |
NB_QUERY_CLIENT_ID |
string | Yes (if NB_ENABLE_AUTH is set to true) |
- | 46923719231972-dhsahgasl3123.apps.googleusercontent.com |
NB_API_QUERY_URL
You'll need to set the NB_API_QUERY_URL environment variable required to run the query tool. NB_API_QUERY_URL is the Neurobagel API URL that the query tool uses to send requests to for results.
NB_QUERY_APP_BASE_PATH
If you are using a custom configuration where the query tool is accessible via a path other than the root (/), you need to set the NB_QUERY_APP_BASE_PATH to your custom path. This ensures that the query tool is correctly rendered and accessible at the specified URL
NB_ENABLE_AUTH
If the API you'd like to send queries to requires authentication, you need to set NB_ENABLE_AUTH to true as it is false by default. This will enable authentication flow of the app.
NB_QUERY_CLIENT_ID
If the NB_ENABLE_AUTH is set to true (it is false by default), you need to provide a valid client ID for the authentication.
At the moment, query tool uses Google for authentication, so you need to obtain a client ID from Google developer console. See documentation for more information.
Set the environment variables
To set environment variables, create a .env file in the root directory and add the environment variables there. If you're running a neurobagel node-API locally on your machine (following the instructions here), your .env file would look something like this:
NB_API_QUERY_URL=http://localhost:8000/
if you're using the remote api, your .env file would look something like this:
NB_API_QUERY_URL=https://federate.neurobagel.org/
if you're using a remote api with authentication, your .env file would look something like this:
NB_API_QUERY_URL=https://federate.neurobagel.org/
NB_ENABLE_AUTH=true
NB_QUERY_CLIENT_ID=46923719231972-dhsahgasl3123.apps.googleusercontent.com
The protocol matters here.
If you wish to use the Neurobagel remote API, ensure your NB_API_QUERY_URL uses https instead of http.
Docker installation
To obtain the query tool docker image, simply run the following command in your terminal:
docker pull neurobagel/query_tool:latest
This Docker image includes the latest release of the query tool and a minimal http server to serve the static tool.
To launch the query tool Docker container and pass in the .env file you have created, simply run
docker run -p 5173:5173 --env-file=.env neurobagel/query_tool:latest
Then you can access the query tool at http://localhost:5173
Note: the query tool is listening on port 5173 inside the docker container,
replace port 5173 by the port you would like to expose to the host.
For example if you'd like to run the tool on port 8000 of your machine you can run the following command:
docker run -p 8000:5173 --env-file=.env neurobagel/query_tool:latest
Manual installation
To install the query tool directly, you'll need node package manager (npm) and Node.js. You can find the instructions on installing npm and node in the official documentation.
Once you have npm and node installed, you'll need to install the dependencies outlined in the package.json file. You can do so by running the following command:
npm install
To launch the tool in developer mode run the following command:
npm run dev
You can also build and then run the tool from (production) build of the application by running the following command:
npm run build && npm run preview
You can verify the tool is running by watching for the` info messages from Vite regarding environment, rendering, and what port the tool is running on in your terminal.
Developer setup
Having installed the dependencies, run the following command to enable husky pre-commit and post-merge hooks:
npx husky install
Docker compose testing environment for development
Since the query tool relies on other neurobagel tools to function, their presence is often required during development. To facilitate this, a docker compose containing a complete testing environment has been created. To use it follow the steps below:
- Install
recipesandneurobagel_examplessubmodules:
git submodule init
git submodule update
- Pull the latest images and bring up the stack using the
testprofile:
docker compose --profile test pull && docker compose --profile test up -d
NOTE: Make sure your .env file in the root directory doesn't contain any of the environment variables used in the docker compose file as it will conflict with the configuration, since docker compose will try to use .env by default.
Usage
To define a cohort, set your inclusion criteria using the following:
- Age: Minimum and/or maximum age (in years) of participant that should be included in the results.
- Sex: Sex of participant that should be included in the results.
- Diagnosis: Diagnosis of participant that should be included in the results
- Healthy control: Whether healthy participants should be included in the results. Once healthy control checkbox is selected, diagnosis field will be disabled since a participant cannot be both a healthy control and have a diagnosis.
- Minimum number of imaging sessions: Minimum number of imaging sessions that participant should have to be included in the results.
- Minimum number of phenotypic sessions: Minimum number of phenotypic sessions that participant should have to be included in the results.
- Assessment tool: Non-imaging assessment completed by participant that should be included in the results.
- Imaging modality: Imaging modality of participant scans that should be included in the results.
- Pipeline name: Name of the pipeline used to process subject scans.
- Pipeline version: Version of the pipeline used to process subject scans.
Once you've defined your criteria, submit them as a query and the query tool will display the results.\
Downloading query results
For a given query, there are two formats of query results that users can download as a TSV file. At least one dataset matching the query must be selected in the results panel in order to download the query results.
Descriptive harmonized tabular data (.tsv)
The default TSV available for download describes the available harmonized attributes and metadata for subjects matching the query, from the (selected) matching datasets. Harmonized data are provided as standardized vocabulary-derived labels for readability.
Each row corresponds to a single matching subject session, except for datasets configured to only return aggregate results.
Example query result TSV
| DatasetName | PortalURI | NumMatchingSubjects | SubjectID | SessionID | SessionFilePath | SessionType | Age | Sex | Diagnosis | Assessment | NumMatchingPhenotypicSessions | NumMatchingImagingSessions | SessionImagingModalities | SessionCompletedPipelines | DatasetImagingModalities | DatasetPipelines |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-01 | ses-01 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-01 | Imaging | nan | nan | nan | nan | 2 | 2 | T1 Weighted, Flow Weighted | fmriprep 23.1.3, freesurfer 7.3.2 | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-01 | ses-01 | nan | Phenotypic | 34.1 | female | nan | Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale | 2 | 2 | nan | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-01 | ses-02 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-02 | Imaging | nan | nan | nan | nan | 2 | 2 | T1 Weighted, Flow Weighted | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-01 | ses-02 | nan | Phenotypic | 35.3 | female | nan | Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale | 2 | 2 | nan | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-02 | ses-01 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-02/ses-01 | Imaging | nan | nan | nan | nan | 2 | 2 | T1 Weighted, Flow Weighted | fmriprep 23.1.3, freesurfer 7.3.2 | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-02 | ses-01 | nan | Phenotypic | nan | male | Attention deficit hyperactivity disorder | Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale | 2 | 2 | nan | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-02 | ses-02 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-02/ses-02 | Imaging | nan | nan | nan | nan | 2 | 2 | T1 Weighted, Flow Weighted | freesurfer 7.3.2 | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-02 | ses-02 | nan | Phenotypic | 39 | male | Attention deficit hyperactivity disorder | Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale | 2 | 2 | nan | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-03 | ses-01 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-03/ses-01 | Imaging | nan | nan | nan | nan | 2 | 2 | T1 Weighted, Flow Weighted | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-03 | ses-01 | nan | Phenotypic | 22.1 | nan | nan | Montreal Cognitive Assessment | 2 | 2 | nan | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-03 | ses-02 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-03/ses-02 | Imaging | nan | nan | nan | nan | 2 | 2 | T1 Weighted, Flow Weighted | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-03 | ses-02 | nan | Phenotypic | 23.2 | nan | Attention deficit hyperactivity disorder | Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale | 2 | 2 | nan | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-04 | ses-01 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-04/ses-01 | Imaging | nan | nan | nan | nan | 2 | 2 | T1 Weighted, Flow Weighted | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-04 | ses-01 | nan | Phenotypic | 21.1 | female | nan | Unified Parkinson's Disease Rating Scale | 2 | 2 | nan | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-04 | ses-02 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-04/ses-02 | Imaging | nan | nan | nan | nan | 2 | 2 | T1 Weighted, Flow Weighted | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-04 | ses-02 | nan | Phenotypic | 22.3 | female | nan | Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale | 2 | 2 | nan | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-05 | ses-01 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-05/ses-01 | Imaging | nan | nan | nan | nan | 2 | 2 | T1 Weighted, Flow Weighted | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-05 | ses-01 | nan | Phenotypic | 42.5 | male | Attention deficit hyperactivity disorder | Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale | 2 | 2 | nan | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-05 | ses-02 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-05/ses-02 | Imaging | nan | nan | nan | nan | 2 | 2 | T1 Weighted, Flow Weighted | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | 5 | sub-05 | ses-02 | nan | Phenotypic | 43.2 | male | Attention deficit hyperactivity disorder | Montreal Cognitive Assessment, Unified Parkinson's Disease Rating Scale | 2 | 2 | nan | nan | Flow Weighted, T1 Weighted | fmriprep 23.1.3, freesurfer 7.3.2 |
| Balloon Analog Risk-taking Task | https://github.com/OpenNeuroDatasets-JSONLD/ds000001.git | 10 | protected | protected | protected | protected | protected | protected | protected | protected | protected | protected | protected | protected | Flow Weighted, T1 Weighted, T2 Weighted | nan |
| Classification learning | https://github.com/OpenNeuroDatasets-JSONLD/ds000002.git | 10 | protected | protected | protected | protected | protected | protected | protected | protected | protected | protected | protected | protected | Flow Weighted, T1 Weighted, T2 Weighted | nan |
Columns in the TSV are described below: * = required values
| Column name | Description |
|---|---|
| DatasetName * | name of the dataset |
| PortalURI | URL to a website or page about the dataset |
| NumMatchingSubjects * | (dataset-level) total number of subjects matching the query in the dataset |
| SubjectID * | subject label |
| SessionID * | session label |
| SessionFilePath | (imaging sessions only) path to the session directory, or subject directory if only one session exists. Either an absolute path from the filesystem root where the dataset is stored, or a relative path from the dataset root for DataLad datasets. |
| SessionType * | type of data acquired in the session, either ImagingSession or PhenotypicSession. Represents the nature of data being described, without denoting specific time or visits. e.g., A session in which both imaging and non-imaging data were acquired would be represented by separate rows, one per type. |
| Age | subject age |
| Sex | subject sex |
| Diagnosis | list of diagnoses for subject |
| Assessment | list of assessments completed by subject |
| NumMatchingPhenotypicSessions * | (subject-level) total number of phenotypic sessions for the subject which match the query |
| NumMatchingImagingSessions * | (subject-level) total number of imaging sessions for the subject which match the query |
| SessionImagingModalities | (imaging sessions only) imaging modalities acquired in the session |
| SessionCompletedPipelines | (imaging sessions only) processing pipelines completed for the session |
| DatasetImagingModalities | (dataset-level) imaging modalities acquired in at least one session in the dataset |
| DatasetPipelines | (dataset-level) processing pipelines completed for at least one session in the dataset |
Machine-optimized harmonized tabular data (.tsv)
A machine-optimized version of the query results, containing URIs instead of descriptive labels for harmonized attributes and metadata of matching subjects, is also available for download as a TSV.
After your query, click the How to get data button, then click the button in the pop-up window to download the TSV.
Each row corresponds to a single matching subject session, except for datasets configured to only return aggregate results.
Example query result TSV
| DatasetName | PortalURI | SubjectID | SessionID | SessionFilePath | SessionType | NumMatchingPhenotypicSessions | NumMatchingImagingSessions | SessionImagingModalities | SessionCompletedPipelines | DatasetImagingModalities | DatasetPipelines |
|---|---|---|---|---|---|---|---|---|---|---|---|
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-01 | ses-01 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-01 | http://neurobagel.org/vocab/ImagingSession | 2 | 2 | http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-01 | ses-01 | nan | http://neurobagel.org/vocab/PhenotypicSession | 2 | 2 | nan | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-01 | ses-02 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-01/ses-02 | http://neurobagel.org/vocab/ImagingSession | 2 | 2 | http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-01 | ses-02 | nan | http://neurobagel.org/vocab/PhenotypicSession | 2 | 2 | nan | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-02 | ses-01 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-02/ses-01 | http://neurobagel.org/vocab/ImagingSession | 2 | 2 | http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-02 | ses-01 | nan | http://neurobagel.org/vocab/PhenotypicSession | 2 | 2 | nan | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-02 | ses-02 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-02/ses-02 | http://neurobagel.org/vocab/ImagingSession | 2 | 2 | http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-02 | ses-02 | nan | http://neurobagel.org/vocab/PhenotypicSession | 2 | 2 | nan | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-03 | ses-01 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-03/ses-01 | http://neurobagel.org/vocab/ImagingSession | 2 | 2 | http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-03 | ses-01 | nan | http://neurobagel.org/vocab/PhenotypicSession | 2 | 2 | nan | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-03 | ses-02 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-03/ses-02 | http://neurobagel.org/vocab/ImagingSession | 2 | 2 | http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-03 | ses-02 | nan | http://neurobagel.org/vocab/PhenotypicSession | 2 | 2 | nan | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-04 | ses-01 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-04/ses-01 | http://neurobagel.org/vocab/ImagingSession | 2 | 2 | http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-04 | ses-01 | nan | http://neurobagel.org/vocab/PhenotypicSession | 2 | 2 | nan | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-04 | ses-02 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-04/ses-02 | http://neurobagel.org/vocab/ImagingSession | 2 | 2 | http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-04 | ses-02 | nan | http://neurobagel.org/vocab/PhenotypicSession | 2 | 2 | nan | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-05 | ses-01 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-05/ses-01 | http://neurobagel.org/vocab/ImagingSession | 2 | 2 | http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-05 | ses-01 | nan | http://neurobagel.org/vocab/PhenotypicSession | 2 | 2 | nan | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-05 | ses-02 | /data/neurobagel/bagel-cli/bids-examples/synthetic/sub-05/ses-02 | http://neurobagel.org/vocab/ImagingSession | 2 | 2 | http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#FlowWeighted | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| BIDS synthetic | https://github.com/bids-standard/bids-examples | sub-05 | ses-02 | nan | http://neurobagel.org/vocab/PhenotypicSession | 2 | 2 | nan | nan | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted | https://github.com/nipoppy/pipeline-catalog/tree/main/processing/fmriprep 23.1.3, https://github.com/nipoppy/pipeline-catalog/tree/main/processing/freesurfer 7.3.2 |
| Balloon Analog Risk-taking Task | https://github.com/OpenNeuroDatasets-JSONLD/ds000001.git | protected | protected | protected | protected | protected | protected | protected | protected | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#T2Weighted | nan |
| Classification learning | https://github.com/OpenNeuroDatasets-JSONLD/ds000002.git | protected | protected | protected | protected | protected | protected | protected | protected | http://purl.org/nidash/nidm#FlowWeighted, http://purl.org/nidash/nidm#T1Weighted, http://purl.org/nidash/nidm#T2Weighted | nan |
Columns in the TSV are described below: * = required values
| Column name | Description |
|---|---|
| DatasetName * | name of the dataset |
| PortalURI | URL to a website or page about the dataset |
| SubjectID * | subject label |
| SessionID * | session label |
| SessionFilePath | (imaging sessions only) path to the session directory, or subject directory if only one session exists. Either an absolute path from the filesystem root where the dataset is stored, or a relative path from the dataset root for DataLad datasets. |
| SessionType * | type of data acquired in the session, either ImagingSession or PhenotypicSession. Represents the nature of data being described, without denoting specific time or visits. e.g., A session in which both imaging and non-imaging data were acquired would be represented by separate rows, one per type. |
| NumMatchingPhenotypicSessions * | (subject-level) total number of phenotypic sessions for the subject which match the query |
| NumMatchingImagingSessions * | (subject-level) total number of imaging sessions for the subject which match the query |
| SessionImagingModalities | (imaging sessions only) imaging modalities acquired in the session, as URIs |
| SessionCompletedPipelines | (imaging sessions only) processing pipelines completed for the session, as URIs |
| DatasetImagingModalities | (dataset-level) imaging modalities acquired in at least one session in the dataset, as URIs |
| DatasetPipelines | (dataset-level) processing pipelines completed for at least one session in the dataset, as URIs |
protected subject-level results for aggregate datasets
Example
For examples of aggregated matching dataset results, see the last rows of the example query result TSV in the previous two sections.
A row in a query result TSV may show protected for all columns except for DatasetName, PortalURI, and other dataset-level columns. This means the source graph database (node) has been configured (via its corresponding Neurobagel node API) to return only aggregate information about matching subjects e.g., for data privacy reasons.
More information on this configuration setting, called NB_RETURN_AGG, and how to change it for a node can be found here.
Testing
The query tool utilizes Cypress framework for testing.
To run the tests execute the following command:
npx cypress open
License
The query tool is released under the terms of the MIT License