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Software Pipeline for Midsagittal Corpus Callosum Thickness Profile Processing

Automated Segmentation, Manual Editor, Thickness Profile Generator, Group-Wise Statistical Comparison and Results Display

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Abstract

This paper presents a fully automated pipeline for thickness profile evaluation and analysis of the human corpus callosum (CC) in 3D structural T 1-weighted magnetic resonance images. The pipeline performs the following sequence of steps: midsagittal plane extraction, CC segmentation algorithm, quality control tool, thickness profile generation, statistical analysis and results figure generator. The CC segmentation algorithm is a novel technique that is based on a template-based initialisation with refinement using mathematical morphology operations. The algorithm is demonstrated to have high segmentation accuracy when compared to manual segmentations on two large, publicly available datasets. Additionally, the resultant thickness profiles generated from the automated segmentations are shown to be highly correlated to those generated from the ground truth segmentations. The manual editing tool provides a user-friendly environment for correction of errors and quality control. Statistical analysis and a novel figure generator are provided to facilitate group-wise morphological analysis of the CC.

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Acknowledgments

This research was conducted within the Developmental Imaging research group, Murdoch Childrens Research Institute at the Children’s MRI Centre, Royal Children’s Hospital, Melbourne Victoria. It was supported by the Murdoch Childrens Research Institute, Royal Children’s Hospital, The University of Melbourne Department of Paediatrics and the Victorian Government’s Operational Infrastructure Support Program.

Conflict of interests

No authors report any conflicts of interest.

Author information

Authors and Affiliations

  1. Royal Childrens Hospital, 50 Flemington Road Parkville, VIC, Melbourne, 3052, Australia

    Chris Adamson, Richard Beare & Marc Seal

  2. Royal Melbourne Hospital, 300 Grattan Street Parkville, VIC, Melbourne, 3050, Australia

    Mark Walterfang

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  1. Chris Adamson
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  2. Richard Beare
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  3. Mark Walterfang
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  4. Marc Seal
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Corresponding author

Correspondence to Chris Adamson.

Additional information

Information Sharing Statement

The Corpus Callosum Thickness Profile Analysis Pipeline (RRID:nlx 157716) software is available at the following URL: https://www.nitrc.org/projects/ccsegthickness. There is a downloadable user guide in PDF format on the website.

Appendix

Appendix

This appendix defines the morphological operations of dilation, erosion, opening, closing. All of these are greyscale with the binary image being a special case of pixels with greyscale values of 0 or 1. Greyscale dilation and erosion for each image pixel x and structuring element SE are defined as:

$$ (I \ensuremath{\oplus} \ensuremath{\text{SE}})(x) = \underset{b \in \ensuremath{\text{SE}}}{\max}I(x + b)$$
(1)
$$ (I \ensuremath{\ominus} \ensuremath{\text{SE}})(x) = \underset{b \in \ensuremath{\text{SE}}}{\min}I(x + b) $$
(2)

for brevity the pixel indices will be dropped, i.e. I ⊕ SE and I ⊖ SE will be used for (1) and (2) respectively.

Morphological opening and closing are defined as follows:

$$ I \ensuremath{\circ} \ensuremath{\text{SE}} = (I \ensuremath{\ominus} \ensuremath{\text{SE}}) \ensuremath{\oplus} \ensuremath{\text{SE}}$$
(3)
$$ I \ensuremath{\bullet} \ensuremath{\text{SE}} = (I \ensuremath{\oplus} \ensuremath{\text{SE}}) \ensuremath{\ominus} \ensuremath{\text{SE}} $$
(4)

The standard structuring elements used in this paper are as follows: disk D r , box B r , where r denotes the radius or size. Let the structuring element Z ϕ be a thin ellipse whose major axis forms the angle ϕ with the x axis.

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Adamson, C., Beare, R., Walterfang, M. et al. Software Pipeline for Midsagittal Corpus Callosum Thickness Profile Processing. Neuroinform 12, 595–614 (2014). https://doi.org/10.1007/s12021-014-9236-3

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