qStudy

A web app to conduct studies for medical images made using magic of 3d slicer, VNC and web apps.

Installation

To proceed with installation docker and docker-compose are required.

Build the docker image from the docker-compose.yml file as follows:

docker-compose build

Usage

1. Create a data direcotry and move all the DICOM files (.nii.gz files) to that data folder. Also, add db_nii.csv file to data directory with UID and DICOM file path for each data file inside the data directory.

   A sample of the db_nii.csv file should look like

   uid,filepath
   1.2.3.4.5,/root/data/1.2.3.4.5.nii.gz
   

   We mount this data volume to the data directory inside the docker container.

2. Create and run a docker container based on the docker image we build.

   Run with logs.

   docker-compose up.
   

   Run in the detached mode.

   docker-compose up -d
   

3. Once docker container is up and running, 3d slicer can be accessed via VNC viewer at 127.0.0.1:5900.

   

   Note: The default password for VNC viewer is vncpassword@123 which can be configured in docker-compose.yml before building a docker image.

4. Open a new tab in the terminal and interact with the Flask API. We can load data into the 3d slicer tool as follows:

   

   Note: In case of a failure or issues faced, perform docker-compose down and docker-compose up.