ThomasSegmentation

Generated the thalamic segmentation using the THOMAS atlas. This component currently requires the Docker desktop application to run the THOMAS segmentation. This is a 41gb download. Follow the instructions on the hipsthomasdocker GitHub page for installation.

On Windows, this component requires an Ubuntu subsystem running with WSL2. If you followed the tutorial on installing Freesurfer4Windows, you should already have this configured. Alternately, you can see a tutorial on configuring Docker Desktop to use WSL2 here. Note that, for some reason, using Docker with WSL2 unnecessarily takes up a ton of hard drive space. I was able to mitigate this problem by first disabling SBOM indexing and experimental features in the Docker Desktop settings, and then following this tutorial to reduce the size of the virtual disk allocated by WSL2 and then running wsl --manage docker-desktop-data --set-sparse true in Windows Powershell. After these steps have been taken, follow the instructions on the hipsthomasdocker GitHub page for installation.

You may run into issues on Windows if Ubuntu or Docker are set up to use WSL1. You can check this by running wsl -list -verbose in Windows Powershell, followed by wsl --set-version <distro-name> 2 to upgrade the distribution to WSL2.

If you are using this component in conjunction with CalculateDistanceToVolumeLabel or LabelVolume2Surface, consider setting LoadLUTFile to 'thomas' in the pipeline for those components to use the correct atlas labels.

Dependencies

• hipsthomasdocker

Inputs and Outputs

• Inputs: MRI

• Outputs: Left Thalamus Identifier, Right Thalamus Identifier, Segmentation Path

Settings

MRIIdentifier

Default: MRI

LeftVolumeIdentifier

Data Identifier for Left Thalamus Default: LThomasVolume

RightVolumeIdentifier

Data Identifier for Right Thalamus Default: RThomasVolume

SegmentationPathIdentifier

Name for the PathInformation data output. Default: SegmentationPath

XML Example

Generates the segmentation for the MRI using the THOMAS atlas. For more information about the THOMAS atlas check out the THOMAS documentation here.

<Component Type="ThomasSegmentation">
    <Name>"Thomas Segmentation FGATIR"</Name>
    <MRIIdentifier>"FGATIR"</MRIIdentifier>
    <LeftVolumeIdentifier>"LThomasVolumeFGATIR"</LeftVolumeIdentifier>
    <RightVolumeIdentifier>"RThomasVolumeFGATIR"</RightVolumeIdentifier>
</Component>