Installation

This page provides a step-by-step overview of creating a virtual environment, installing DOSMA via pip, and verifying the install.

Anaconda

Please install the Anaconda virtual environment manager.

Setup

The following steps will create an Anaconda environment (dosma_env).

  1. Open a Terminal/Shell window

  2. Create the dosma_env environment:

    $ conda create -n dosma_env python=3.7

  3. Install dosma via pip:

    $ pip install dosma

  4. Complete the DOSMA questionnaire.

If you want to update your dosma version, run pip install --upgrade dosma.

Segmentation

DOSMA currently supports automatic deep learning segmentation methods. These methods use pre-trained weights for segmenting tissues in specific scans. Currently, segmentation for quantitative double echo in steady state (qDESS) scans is supported for knee articular cartilage and meniscus.

If you will be using this functionality, please follow the instructions below.

  1. Request access using this Google form and email arjundd (at) <standard Stanford email domain>

  2. Save these weights in an accessible location. Do not rename these files.

We understand this process may be involved and are actively working on more effective methods to distribute these weights.

Registration

Registration between scans in DOSMA is supported through Elastix and Transformix. If you plan on using the registration, follow the instructions below:

  1. Download elastix

  2. Follow instructions on adding elastix/transformix to your system path

On Ubuntu 18.04 Elastix version 5.0.1 does not work properly. Elastix 4.9.0 is recommended.

If you are using a MacOS system, you may run into path issues with elastix (see this discussion). To fix this, we can use the dosma.symlink_elastix to create appropriate symbolic links to files causing issues:

$ conda activate dosma_env; python >>> from dosma import symlink_elastix >>> symlink_elastix()

Note you will need to run this every time you update elastix/transformix paths on your machine.

Verification

  1. Open new Terminal window.

  2. Activate DOSMA Anaconda environment:

    $ conda activate dosma_env

  3. Run DOSMA from the command-line (cli). You should see a help menu output:

    $ python -m dosma.cli --help

  4. Run DOSMA as an UI application (app). You should see a UI window pop-up:

    $ python -m dosma.app

Updating DOSMA

If you have used an earlier stand-alone of DOSMA (v0.0.11 or earlier), you may already have a dosma_env virtual environment. Please delete this environment and reinstall follows steps in setup Setup.

For those (v0.0.12 or later) having installed dosma via pip, you can update dosma using:

$ pip install --upgrade dosma