Cloud ASHS Tutorial: T2-MRI¶

This tutorial assumes that you are using the ASHS-PMC atlas. Make sure that your MRI data is compatible with this atlas. The procedure is nearly identical for other ASHS atlases based on the combination of T2-weighted and T1-weighted MRI.

1. Create an ITK-SNAP workspace¶

To send your images to the cloud, you need to create an ITK-SNAP workspace that contains the T2-weighted and T1-weighted images.

• Open ITK-SNAP
• Use File->Open Main Image... to load the T2-weighted image as the main image
• Use File->Add Another Image... to load the T1-weighted image as the secondary image
• If the T2 and T1-weighted MRI scans are poorly aligned, perform registration using the interactive tools (Tools->Registration)
  • See also the ITK-SNAP registration video
• Save the ITK-SNAP workspace to a file using Workspace->Save Workspace

2. Log in to the Distributed Segmentation Service (DSS)¶

Next, you need to log in to the DSS server. This requires a Google account.

• Open the DSS window using Tools->Distributed Segmentation Service
• Select the "Connect" tab if it is not already selected
• Press the Get Token button. This opens a web browser at the DSS login page, shown below.
  • Follow the login prompts on the website. Once you log in with your Google account, you will see a 40-character login token. Copy the token and paste it back into ITK-SNAP.
• The ITK-SNAP DSS window should show an updated status, in green, indicating that you have logged in
  • The next time you open ITK-SNAP on the same device, your login information will be remembered and you will not need to repeat the token-based login.

3. Upload your workspace and create a ticket¶

In this step, you send your workspace to the cloud for segmentation with ASHS.

• Select the "Submit" tab in the ITK-SNAP DSS window
• Select the service you wish to use. In this example, we use the ASHS-PMC service. The image specifications for this service are described here.
• In the table of "tags", make sure that the correct images are assigned to the "T2-MRI" and "T1-MRI" tags
  • Ignore the AC/PC landmarks in the table. These are not yet supported.
• Press Submit. The workspace will be uploaded to the server and a new ticket will be created.

4. Monitor ticket status¶

Once a ticket is created, the DSS window switches to the "Results" tab, where you can monitor the progress of your ticket. While the ticket is being processed, you can close ITK-SNAP or submit additional tickets.

• Your ticket is highlighted in the list of tickets on the left of the window, and its progress is shown on the right.
• Note the status of your ticket:
  • ready: the ticket has been uploaded and is in the queue to be processed
  • claimed: the ticket is being processed
  • success: the ticket was processed successfully and results are available
  • failed/timed out: an error occurred while servicing the ticket
• Once your ticket is in the claimed state, log messages show the progress of the ASHS segmentation. Some log messages have attachments in the form of QC (quality control) images. Click the attachment button to list the attachments and open them in a web browser.
• To abort ticket processing, press the Delete button

5. Download and examine ASHS results¶

Once a ticket completes successfully, you can download the results as an ITK-SNAP workspace.

• Select a ticket that is in the success state and press the Download button
  • A dialog like the one shown below will appear.
  • Choose where to save the result workspace and whether to open it after downloading.
• The workspace contains multiple segmentation layers. You can access the different segmentation layers using the Layer Inspector in ITK-SNAP (Tools->Layer Inspector).
  • Use the ++braces-left++ and ++braces-right++ keys to switch between segmentation layers quickly
  • See the table below for an explanation of each layer.

See the equivalent page for HyperASHS.