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Cloud ASHS Tutorial: T2-MRI

This page has moved. The ASHS documentation is now at ashs.itksnap.org. Go to the new version of this page: https://ashs.itksnap.org/ashs/cloud/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.

In order to use this service, you will need install ITK-SNAP 3.8-BETA version (downloaded the version suitable for your operation system here).

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 you notice that the T2 and T1-weighted MRI scans are poorly aligned, perform registration using interactive tools ("Tools->Registration")
- See also ITK-SNAP registration video
Save the ITK-SNAP workspace to a file using "Workspace->Save Workspace"

ITK-SNAP with a T2-weighted image loaded as the main image and the T1-weighted image loaded as the additional image.

2. Login to the Distributed Segmentation System (DSS)

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

Open the DSS window using "Tools->Distributed Segmentation Service"
Select the "Connect" tab if not already selected
Press the "Get Token" button. This will open a web browser and take you to the login page for DSS, shown to the right.
- Follow the login prompts on the website. Once you login 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 successfully logged into the system
- Next time you open ITK-SNAP on the same device, your login information will be saved. You will not need to repeat the token-based login process.

The ITK-SNAP distributed segmentation system (DSS) window, configuration tab. Press 'Get Token' to login.

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

3. Upload Your Workspace and Create a Ticket

In this step, you will 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 are using 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, as in the example on the right.
- 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.

Creating a ticket

4. Monitoring Ticket Status

Once a ticket is created, the DSS window will switch 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 will be highlighted in the list of tickets on the left of the window, and the progress of your ticket will be 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 actively being processed
- success: the ticket was successfully processed and results are available
- failed/timed out: an error occurred while servicing the ticket
Once your ticket is in claimed state, log messages show the progress of 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

Clicking on one of the attachments shows intermediate results (registration between ASHS template, T1-MRI and T2-MRI)

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 success state and press the "Download" button
- A dialog shown on the right will appear.
- Choose where to save the result workspace and whether to open it after downloading.
The workspace will contain multiple segmentation layers. You can access the different segmentation layers using the Layer Inspector in ITK-SNAP ("Tools->Layer Inspector").
- Use the keys '{' and '}' to switch segmentation layers quickly
- See the table below for an explanation.

After pressing 'Download', select the location where the the result workspace will be saved, and whether to open it

Viewing segmentation results in ITK-SNAP

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