Identifying errors in Freesurfer automated skull stripping and the incremental utility of manual intervention

Brain Imaging and Behavior
Abigail B WatersDavid A Gansler

Abstract

Quality assurance (QA) is vital for ensuring the integrity of processed neuroimaging data for use in clinical neurosciences research. Manual QA (visual inspection) of processed brains for cortical surface reconstruction errors is resource-intensive, particularly with large datasets. Several semi-automated QA tools use quantitative detection of subjects for editing based on outlier brain regions. There were two project goals: (1) evaluate the assumption that statistical outliers are related to errors of cortical extension, and (2) examine whether error identification and correction significantly impacts estimation of cortical parameters and established brain-behavior relationships. T1 MPRAGE images (N = 530) of healthy adults were obtained from the NKI-Rockland Sample and reconstructed using Freesurfer 5.3. Visual inspection of T1 images was conducted for: (1) participants (n = 110) with outlier values (z scores ±3 SD) for subcortical and cortical segmentation volumes (outlier group), and (2) a random sample of remaining participants (n = 110) with segmentation values that did not meet the outlier criterion (non-outlier group). The outlier group had 21% more participants with visual inspection-identified errors than participants...Continue Reading

References

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Jun 14, 2005·Biological Psychiatry·Larry J SeidmanNikos Makris
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Nov 6, 2015·Frontiers in Neuroscience·Christopher S McCarthyWendy R Kates

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Citations

May 1, 2019·ELife·Kayle S SawyerMarlene Oscar-Berman
Aug 28, 2019·Scientific Reports·Farshid SepehrbandArthur W Toga
May 6, 2019·Neuroinformatics·Shaina Sta CruzFarshid Sepehrband
Jan 21, 2021·Movement Disorders : Official Journal of the Movement Disorder Society·Erin K DonahueFarshid Sepehrband
Apr 20, 2021·Journal of Alzheimer's Disease : JAD·Helena M BlumenJoe Verghese
Mar 26, 2021·The European Journal of Neuroscience·Isabella Hoi Kei LeungShantel Leigh Duffy

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Methods Mentioned

BETA
imaging techniques

Software Mentioned

QATools for Freesurfer
MPRAGE
Freeview
FreeSurfer
NKI

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