NiftyOne is a platform for bulk visualization of large-scale neuroimaging datasets. It is built with FiftyOne.

• NiftyOne
  • Installation
  • Testing
  • Usage
  • Running NiftyOne on a remote cluster
  • FAQ

1. Install conda For stability, NiftyOne should be installed in it's own environment. For example,

conda create -y -n niftyone python=3.10
conda activate niftyone

pip install -U pip
pip install git+https://github.com/cmi-dair/niftyone.git

1. Install datalad to download the data files
2. You can use whatever BIDS dataset (such as ds000102 from OpenNeuro) as an example to test

niftyone bids_dir output_dir participant --workers 8

niftyone app launch

niftyone bids_dir output_dir participant --workers 8

niftyone bids_dir output_dir group

niftyone bids_dir output_dir launch

from a Mac/Linux/Windows Powershell terminal:

ssh [email protected]

e.g. interact

At this point you should see "App Launched" in your terminal with a localhost URL.

Open a second terminal.

Execute the following command to create a multihop port forward from your local machine --> login node --> compute node. Related gist

HOST=(name of compute node, not the full address. e.g. r001) PORT=5151

ssh -L $PORT:localhost:$PORT [email protected] ssh -L $PORT:localhost:$PORT -N $HOST

https://superuser.com/questions/1154383/ssh-port-forwarding-on-windows

https://phoenixnap.com/kb/ssh-port-forwarding

NiftyOne can be installed both locally and on a remote server. If NiftyOne is installed on a server, the output can be viewed from a local web browser after port fowarding.

Try testing with a simple HTTP server with a "Hello World" HTML file using port fowarding to rule out any networking problems before installing further software.

$python3 -m http.server 9000

https://www.digitalocean.com/community/tutorials/python-simplehttpserver-http-server#python-simplehttpserver-error-no-module-named-simplehttpserver

/home/user/.../mongod: error while loading shared libraries

Try re-installing mongo and re-creating the virtual conda environment.

OSError: You must have fiftyone>=0.22.1 installed in order to migrate from v0.22.1 to v0.21.6, but you are currently running fiftyone==0.21.6.

Try re-installing fiftyone / niftyone

Try incrementing to port 5152, 5153, etc