Cloud ASHS Command-Line Tutorial

Step 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. Here we create the workspace using command-line tools. You can also create the workspace using the ITK-SNAP GUI.

We assume that your MRI scans are named t2_oblique.nii and t1_wholebrain.nii and that these files are in the current directory open in your terminal.

Enter the following command to create a workspace containing these files

itksnap-wt -layers-set-main t2_oblique.nii -tags-add T2-MRI \

-layers-add-anat t1_wholebrain.nii -tags-add T1-MRI \

-layers-list -o mywork.itksnap

This command adds the T2 image to a blank workspace and assigns it the tag "T2-MRI", then adds the T1 image as an additional image and assigns it the tag "T1-MRI", prints out the contents of the workspace, and finally saves the workspace to a file called mywork.itksnap.

Create a Ticket for Cloud ASHS

Run the command below to list the services currently available on the cloud:

itksnap-wt -dss-services-list

• The listing of the services (see figure) includes service name, version, description, and a unique code in the second column that identifies each service. Select and copy the code for the ASHS-PMC service (if there are multiple versions, choose the latest one)

The following command will send the workspace to the cloud and will create a numbered "ticket". Instead of [service_code], paste the unique code of the ASHS-PMC service (see figure).

itksnap-wt -i mywork.itksnap -dss-tickets-create [service_code]

• It may take a minute or two for the workspace to be uploaded to the server

• If successful, the number of the ticket will be printed after the 2> prompt

Monitoring Ticket Status

Once a ticket is created, the easiest way to monitor its status is using the following command:

itksnap-wt -dss-tickets-wait [ticket-id]

• When you run this command, it will not return until the ticket has finished running.

  • If you want the command to return immediately, enter 0 after the ticket id.

  • You can always interrupt the command using Control-C key. Doing so will not interrupt the processing of your ticket, just the command that monitors progress.

• The command will present you with log messages and links to image attachments that you can view to see intermediate ASHS results

• You can submit additional tickets while a ticket is being processed

Downloading ASHS Segmentation Results

Once a ticket completes successfully, you can download the results as an ITK-SNAP workspace. You will need to specify the directory where you want the new workspace to be placed.

itksnap-wt -dss-tickets-download [ticket-id] [directory]

• The workspace is saved as an ticket_XXXX.itksnap file that can be opened using the ITK-SNAP GUI