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. Currently has only been tested on MacOS.

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>