FreesurferHippocampalSegmentation

The FreesurferHippocampalSegmentation component attempts to load Freesurfer's hippocampal segmentation or builds the segmentation if it doesn't exist. The Freesurfer documentation for hippocampal subsegmentation suggests that the MATLAB R2014b runtime is required to be installed for Freesurfer to generate the hippocampal subsegmentation; however, it is also possible to use the MATLAB R2019b runtime if you are using Freesurfer 7.3.2. This is important for M1 and M2 Mac users, as the R2014b runtime does not work on the newer Mac architecture. You should be able to follow the same installation instructions as described on the Freesurfer documentation but install the R2019b runtime instead if you would like to generate the hippocampal subsegmentation on M1 and M2 Macs. If you are using VERA on a Windows computer, you will need to install freesurfer 7.2.0 and the MATLAB R2014b runtime to generate the hippocampal segmentation. This is done automatically if you use the Freesurfer4Windows script.

Note that in order to generate the hippocampal segmentation, VERA needs to be able to find the segmentation folder in the subject path. The easiest way to accomplish this is by using the FreesurferModelGeneration component to generate the segmentation through VERA. However, if you already have a segmentation folder you are loading, you can also use the ImportFreesurferSegmentation component to copy the segmentation folder into the VERA project folder.

Inputs and Outputs

• Inputs: None

• OptionalInputs: Path to Freesurfer Segmentation

• Outputs: Volumes representing the left and right hippocampal segmentations (VolumeIdentifiers will be prefixed with 'L' and 'R' respectively)

Settings

VolumeIdentifier

Identifier for Hippocampal volumes. VolumeIdentifiers will be prefixed with 'L' and 'R' respectively.

Default: Hippocampus

SegmentationPathIdentifier

Identifier for the SegmentationPath - if available

Default: SegmentationPath

XML Example

Loads the Hippocampal segmentation and stores it as LHippocampus and RHippocampus.

<Component Type="FreesurferHippocampalSegmentation">
    <Name>"Load or Generate Hippocampal subsegmentations"</Name>
    <VolumeIdentifier>"Hippocampus"</VolumeIdentifier>
</Component>