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The AANsegment tool generates automated segmentations of ten brainstem nuclei that are part of the ascending arousal network in MRI scans. The nuclei which we segment are listed below: ventral tegmental area (VTA) locus coeruleus (LC) dorsal raphe (DR) median raphe (MnR) pontis oralis (PnO) laterodorsal tegmental nucleus (LDTg) parabrachial complex (PBC) periaqueductal grey (PAG) midbrain reticular formation (mRt) pedunculotegmental nucleus (PTg) |
Segmentation of brainstem AAN nuclei
Authors: Mark D. Olchanyi, Juan Eugenio Iglesias, Brian L. Edlow
E-mail(s): olchanyi [at] mit.edu, jiglesiasgonzalez [at] mgh.harvard.edu and bedlow [at] mgh.harvard.edu
Rather than directly contacting the author, please post your questions on this module to the FreeSurfer mailing list at freesurfer [at] nmr.mgh.harvard.edu
If you use these tools in your analysis, please cite:
* Histology-guided MRI segmentation of brainstem nuclei critical to consciousness. Mark David Olchanyi, Jean Augustinack, Robin L Haynes, Laura D Lewis, Nicholas Cicero, Jian Li, Christophe Destrieux, Rebecca D Folkerth, Hannah C Kinney, Bruce Fischl, Emery N Brown, Juan Eugenio Iglesias, Brian L Edlow, medRxiv; doi: https://doi.org/10.1101/2024.09.26.24314117
See also: BrainstemSubstructures, ThalamicNuclei, HippocampalSubfieldsAndNucleiOfAmygdala
Contents
- Motivation and General Description
- Installation
- Tool usage
- Frequently asked questions (FAQ)
1. Motivation and General Description
The AANsegment tool generates automated segmentations of ten brainstem nuclei that are part of the ascending arousal network in MRI scans. The nuclei which we segment are listed below:
ventral tegmental area (VTA) locus coeruleus (LC) dorsal raphe (DR) median raphe (MnR) pontis oralis (PnO) laterodorsal tegmental nucleus (LDTg) parabrachial complex (PBC) periaqueductal grey (PAG) midbrain reticular formation (mRt) pedunculotegmental nucleus (PTg)