FreesurferModelGeneration

Generated the 3D surface using Freesurfer

Dependencies

• Freesurfer

• C drive mounting path if used on Windows with WSL

Inputs and Outputs

• Inputs: T1 MRI

• Outputs: Surface, Left Hemisphere Sphere, Right Hemisphere Sphere, Path to the Segmentation folder within VERA

Settings

MRIIdentifier

Default: MRI

SurfaceIdentifier

Data Identifier for Surface Output Default: Surface

SphereIdentifier

Data Identifier for spherical surface Output. A sphere represents a hemisphere, two outputs will be generated with prefix 'L_' and 'R_' respectively. Default: Sphere

AnnotationType

Surface annotation labels loaded from Freesurfer. Default: aparc

SegmentationPathIdentifier

Name for the PathInformation data output. Default: SegmentationPath

XML Example

Generates the 3D Model for the MRI and loads the Destrieux Atlas annotation. For more information about Freesurfer atlases check out the Freesurfer documentation here.

<Component Type="FreesurferModelGeneration">
    <Name>"Generate Freesurfer Model"</Name>
    <AnnotationType>"aparc"</AnnotationType>
    <MRIIdentifier>"MRI"</MRIIdentifier>
    <SegmentationPathIdentifier>"SegmentationPath"</SegmentationPathIdentifier>
    <SphereIdentifier>"Sphere"</SphereIdentifier>
    <SurfaceIdentifier>"Surface"</SurfaceIdentifier>
    <SurfaceType>"pial"</SurfaceType>
</Component>