FNNDSC/niivue-browser

A NiiVue application for browsing subject data on the filesystem.

Niivue Hemisphere Surface Browser

An opinionated NiiVue application for browsing surface meshes found in a filesystem directory.

Demo: https://niivue-hosting-of-medical-image-analysis-platform-dcb83b.apps.shift.nerc.mghpcc.org/

Usage

Prepare your data to adhere to the naming conventions. Then, run

docker run --rm --name niivue-browser \
    -p 2019:2019 -p 8080:8080 \
    -v "/path/on/host/to/your/data:/data:ro" \
    ghcr.io/fnndsc/niivue-browser:latest

For whatever reason, you can change the container directory where data is served from by setting NIIVUEBROWSER_SUBJECTS_DIR.

docker run --rm --name niivue-browser \
    -p 2019:2019 -p 8080:8080 \
    -e NIIVUEBROWSER_SUBJECTS_DIR=/custom_dir
    -v "/path/on/host/to/your/data:/custom_dir:ro" \
    ghcr.io/fnndsc/niivue-browser:latest

• The application will be available at http://localhost:8080/.
• Prometheus metrics can be read from http://localhost:2019/metrics. See https://caddyserver.com/docs/metrics for more information.

Naming Conventions

• The data directory should contain subdirectories where each subdirectory contains the files for one subject.
• Data files may represent: brain hemisphere volumes, hemisphere masks, hemisphere surfaces, or hemisphere surface data. For example, you could have a white matter surface mesh and sulcal depth data for that surface. Supported file formats include .nii, .nii.gz, and .mz3. We recommend using niivue-browser to convert from MNI formats (.mnc, .obj and .txt).
• Data file names must be prefixed with lh. for left hemispheres or rh. for right hemispheres.
• Associated data files must have the same file name, not considering the lh./rh. prefix nor file extension. For example, lh.wm.mz3 and rh.wm.mz3 will be recognized together as "wm" surfaces. Likewise, lh.wm.disterr.mz3, lh.wm.smtherr.mz3, lh.wm.tlink_10mm.mz3 will be recognized as surface data for the lh.wm.mz3 surface. Rules for file name recognition are coded in src/lib/recognize.ts.
• An optional CSV file can be located in the data directory, which provides details about each subject. This CSV file must have a column titled "subject" (case-insensitive). Other columns may contain arbitrary string data.

Download some sample data:

curl -sf https://stack.nerc.mghpcc.org:13808/swift/v1/AUTH_2dd3b02b267242d9b28f94a512ea9ede/fnndsc-public/samples/fetal_brain/sample_human_fetus_brain_mri_subplate_surfaces.tar.gz | tar xvz

Development

1. Create a directory (or symlink) ./data which contains subdirectories, where each subdirectory contains data for a single subject. Optionally, place a file called ./data/*.csv which provides metadata about subjects.
2. Run pnpm run dev and pnpm run dev:proxy concurrently.
3. In your browser, open up http://localhost:51733/

Deployment

Examples for how to deploy on Kubernetes/OpenShift can be found here:

https://github.com/FNNDSC/NERC/tree/master/niivue-browser