Cloud HyperASHS Tutorial: T1-MRI¶
This tutorial uses the HyperASHS-PMC-T1 service. Make sure that your MRI data is compatible with this model. The procedure is very similar to the one for T2-weighted and T1-weighted MRI.
ITK-SNAP 4.6 or later is required
HyperASHS returns segmentations at a finer resolution than the input MRI, i.e., in a different voxel space from the main image. Only ITK-SNAP 4.6 and later can work with such segmentations, so older versions of ITK-SNAP cannot be used with Cloud HyperASHS.
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
2. Log in to the Distributed Segmentation Service (DSS)¶
Log in to the DSS server with your Google account, exactly as described in step 2 of the T2-MRI tutorial: open Tools->Distributed Segmentation Service, press Get Token, log in on the web page, and paste the token back into ITK-SNAP.
3. Upload your workspace and create a ticket¶
- Select the "Submit" tab in the ITK-SNAP DSS window
- Select the HyperASHS-PMC-T1 service from the list
- Make sure that the T1-weighted image is assigned to the "T1-MRI" tag
- Press Submit. The workspace will be uploaded to the server and a new ticket will be created.
4. Monitor ticket status¶
The DSS window switches to the "Results" tab, where you can monitor the progress of your ticket. The ticket states and QC attachments are described in step 4 of the T2-MRI tutorial.
5. Download and examine the results¶
Once a ticket is in the success state, select it and press Download to save the result workspace and, optionally, open it in ITK-SNAP. See Outputs for a description of the HyperASHS results.
Using classic ASHS? See the equivalent page for ASHS Classic.