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An Open-Source Label Atlas Correction Tool and Preliminary Results on Huntingtons Disease Whole-Brain MRI Atlases

Department of Psychiatry, University of IowaIowa City, IA, USA.
Publication Date:
Front Neuroinform
Volume Number:
Front Neuroinform. 2016 Aug 3;10:29.
PubMed ID:
Huntingtons Disease, ITK, multi-atlas, brain MRI, label atlas, multi-modal, open-source
Appears in Collections:
R01 NS050568/NS/NINDS NIH HHS/United States
R01 EB000975/EB/NIBIB NIH HHS/United States
R01 EB008171/EB/NIBIB NIH HHS/United States
R01 NS040068/NS/NINDS NIH HHS/United States
R01 NS054893/NS/NINDS NIH HHS/United States
P41 RR015241/RR/NCRR NIH HHS/United States
S10 RR023392/RR/NCRR NIH HHS/United States
U54 EB005149/EB/NIBIB NIH HHS/United States
R03 EB008673/EB/NIBIB NIH HHS/United States
Generated Citation:
Forbes J.L., Kim R.E.Y., Paulsen J.S., Johnson H.J. An Open-Source Label Atlas Correction Tool and Preliminary Results on Huntingtons Disease Whole-Brain MRI Atlases. Front Neuroinform. 2016 Aug 3;10:29. PMID: 27536233. PMCID: PMC4971025.
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The creation of high-quality medical imaging reference atlas datasets with consistent dense anatomical region labels is a challenging task. Reference atlases have many uses in medical image applications and are essential components of atlas-based segmentation tools commonly used for producing personalized anatomical measurements for individual subjects. The process of manual identification of anatomical regions by experts is regarded as a so-called gold standard; however, it is usually impractical because of the labor-intensive costs. Further, as the number of regions of interest increases, these manually created atlases often contain many small inconsistently labeled or disconnected regions that need to be identified and corrected. This project proposes an efficient process to drastically reduce the time necessary for manual revision in order to improve atlas label quality. We introduce the LabelAtlasEditor tool, a SimpleITK-based open-source label atlas correction tool distributed within the image visualization software 3D Slicer. LabelAtlasEditor incorporates several 3D Slicer widgets into one consistent interface and provides label-specific correction tools, allowing for rapid identification, navigation, and modification of the small, disconnected erroneous labels within an atlas. The technical details for the implementation and performance of LabelAtlasEditor are demonstrated using an application of improving a set of 20 Huntingtons Disease-specific multi-modal brain atlases. Additionally, we present the advantages and limitations of automatic atlas correction. After the correction of atlas inconsistencies and small, disconnected regions, the number of unidentified voxels for each dataset was reduced on average by 68.48%.

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