Thresholding to remove fluid from FreeSurfer segmentations of quantitative brain maps – a simple solution to a painful problem
Motivation: Segmentation of quantitative maps is required to compute anatomical region mean relaxation times. FreeSurfer is designed to automatically segment conventional weighted images. Voxels of CSF contaminate tissue segmentations in some healthy volunteers, skewing the mean T1 or T2. Goal(s): To remove contaminant fluid from tissue regions of interest in T1 and T2 maps. Approach: Mean T1 or T2 of CSF in ventricles is used as a maximum threshold within brain tissue. Results: Thresholding prior to 2D erosion of masks removes contaminant CSF and prevents erroneous variation between 10 healthy volunteers. Impact: A simple threshold-based correction of FreeSurfer segmentation applied to quantitative T1 and T2 maps. The same threshold can be applied to all subjects in one step, eliminating the need for laborious manual adjustment.
Authors
- Stefanie Thust (ORCID: https://orcid.org/0000-0001-5136-6000)
- Rebecca Quest (ORCID: https://orcid.org/0000-0002-0457-8665)
- Iulius Dragonu
- Peter Lally (ORCID: https://orcid.org/0000-0003-0075-0103)
- Matthew Orton (ORCID: https://orcid.org/0000-0002-0805-763X)
- Simran Kukran
- Mary E. Finnegan (ORCID: https://orcid.org/0000-0001-5655-0886)
- Ben K. Statton (ORCID: https://orcid.org/0000-0001-5118-7977)
- Dow‐Mu Koh (ORCID: https://orcid.org/0000-0001-7654-8011)
- Salvador Cardona (ORCID: https://orcid.org/0000-0002-2882-3098)
- Luke Dixon (ORCID: https://orcid.org/0000-0003-4060-7897)
- Joely Smith (ORCID: https://orcid.org/0000-0002-2382-4219)
- Neal K. Bangerter (ORCID: https://orcid.org/0000-0001-6444-1882)
- Matthew Grech Sollars
Publication Details
- Journal
- Proceedings on CD-ROM - International Society for Magnetic Resonance in Medicine. Scientific Meeting and Exhibition/Proceedings of the International Society for Magnetic Resonance in Medicine, Scientific Meeting and Exhibition
- Published
- 2024-11-26
- DOI
- https://doi.org/10.58530/2024/2134
- Primary Topic
- Advanced Neuroimaging Techniques and Applications
- Type
- article
- Field-Weighted Citation Impact
- 0.00