You are viewing the documentation for classic ASHS

For new projects we recommend HyperASHS, which produces isotropic-resolution segmentations of the same structures and is available in the cloud through ITK-SNAP as well as locally.

Cloud ASHS Tutorial: T1-MRI¶

This tutorial assumes that you are using the ASHS-PMC-T1 atlas. Make sure that your MRI data is compatible with this atlas. The procedure is very similar to the one for ASHS atlases based on T2-weighted and T1-weighted MRI.

Note

To use this service, you need ITK-SNAP 3.8 or later.

1. Create an ITK-SNAP workspace¶

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

Open ITK-SNAP
Use File->Open Main Image... to load the T1-weighted image as the main image
Save the ITK-SNAP workspace to a file using Workspace->Save Workspace

ITK-SNAP with a T1 image loaded — ITK-SNAP with a T1-weighted image loaded as the main image.

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.

DSS window, connect tab — The ITK-SNAP DSS window, configuration tab. Press "Get Token" to log in.

DSS login web page — The login web page. Paste the token into ITK-SNAP.

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-T1 service. The image specifications for this service are described here.
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

Monitoring ticket progress in the DSS window.

QC attachment — Clicking on one of the attachments shows intermediate results.

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 will appear.
- Choose where to save the result workspace and whether to open it after downloading.
Unlike the output of ASHS for T2-MRI, the workspace contains only one segmentation layer: the result of the joint label fusion step (the "JLF result").

Viewing results in ITK-SNAP — Viewing segmentation results in ITK-SNAP.

See the equivalent page for HyperASHS.

T1-MRI Tutorial