• Record: found
  • Abstract: found
  • Article: found
Is Open Access

Merged Group Tractography Evaluation with Selective Automated Group Integrated Tractography

Read this article at

      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.


      Introduction: Tractography analysis in group-based studies across large populations has been difficult to implement. We propose Selective Automated Group Integrated Tractography (SAGIT), an automated group tractography software platform that incorporates multiple diffusion magnetic resonance imaging (dMRI) practices which will allow great accessibility to group-wise dMRI. We use a merged tractography approach that permits evaluation of tractography datasets at the group level. We also introduce an image normalized overlap score (NOS) that measures the quality of the group tractography results. We deploy SAGIT to evaluate deterministic and probabilistic constrained spherical deconvolution (CST det , CST prob ) tractography, eXtended Streamline Tractography (XST), and diffusion tensor tractography (DTT) in their ability to delineate different neuroanatomy, as well as validating NOS across these different brain regions.

      Materials and methods: Magnetic resonance sequences were acquired from 42 healthy adults. Anatomical and group registrations were performed using Automated Normalization Tools. Cortical segmentation was performed using FreeSurfer. Four tractography algorithms were used to delineate six sets of neuroanatomy: fornix, facial/vestibular-cochlear cranial nerve complex, vagus nerve, rubral–cerebellar decussation, optic radiation, and auditory radiation. The tracts were generated both with and without region of interest filters. The generated visual reports were then evaluated by five neuroscientists.

      Results: At a group level, merged tractography demonstrated that different methods have different fiber distribution characteristics. CST prob is prone to false-positives, and thereby suitable in anatomy with strong priors. CST det and XST are more conservative, but have greater difficulty resolving hemispherical decussation and distant crossing projections. DTT consistently shows the worst reproducibility across the anatomies. Linear regression of rater scores against NOS shows significant ( p < 0.05) correlation of the two sets of scores in filtered tractography. However, correlations are not significant ( p > 0.05) for unfiltered tractography.

      Conclusion: The tractography results demonstrated reliable and consistent performance of SAGIT across multiple subjects and techniques. Through SAGIT, we quantifiably demonstrated that different algorithms showed different strengths and weaknesses at a group level. While no single algorithm seems to be suitable for all anatomical tasks, it is useful to consider the use of a mix of algorithms for different anatomical segments. SAGIT appears to be a promising group-wise tractography analysis approach for this purpose.

      Related collections

      Most cited references 30

      • Record: found
      • Abstract: found
      • Article: not found

      Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain.

      We present a technique for automatically assigning a neuroanatomical label to each voxel in an MRI volume based on probabilistic information automatically estimated from a manually labeled training set. In contrast to existing segmentation procedures that only label a small number of tissue classes, the current method assigns one of 37 labels to each voxel, including left and right caudate, putamen, pallidum, thalamus, lateral ventricles, hippocampus, and amygdala. The classification technique employs a registration procedure that is robust to anatomical variability, including the ventricular enlargement typically associated with neurological diseases and aging. The technique is shown to be comparable in accuracy to manual labeling, and of sufficient sensitivity to robustly detect changes in the volume of noncortical structures that presage the onset of probable Alzheimer's disease.
        • Record: found
        • Abstract: found
        • Article: not found

        Probabilistic diffusion tractography with multiple fibre orientations: What can we gain?

        We present a direct extension of probabilistic diffusion tractography to the case of multiple fibre orientations. Using automatic relevance determination, we are able to perform online selection of the number of fibre orientations supported by the data at each voxel, simplifying the problem of tracking in a multi-orientation field. We then apply the identical probabilistic algorithm to tractography in the multi- and single-fibre cases in a number of example systems which have previously been tracked successfully or unsuccessfully with single-fibre tractography. We show that multi-fibre tractography offers significant advantages in sensitivity when tracking non-dominant fibre populations, but does not dramatically change tractography results for the dominant pathways.
          • Record: found
          • Abstract: found
          • Article: not found

          A reproducible evaluation of ANTs similarity metric performance in brain image registration.

          The United States National Institutes of Health (NIH) commit significant support to open-source data and software resources in order to foment reproducibility in the biomedical imaging sciences. Here, we report and evaluate a recent product of this commitment: Advanced Neuroimaging Tools (ANTs), which is approaching its 2.0 release. The ANTs open source software library consists of a suite of state-of-the-art image registration, segmentation and template building tools for quantitative morphometric analysis. In this work, we use ANTs to quantify, for the first time, the impact of similarity metrics on the affine and deformable components of a template-based normalization study. We detail the ANTs implementation of three similarity metrics: squared intensity difference, a new and faster cross-correlation, and voxel-wise mutual information. We then use two-fold cross-validation to compare their performance on openly available, manually labeled, T1-weighted MRI brain image data of 40 subjects (UCLA's LPBA40 dataset). We report evaluation results on cortical and whole brain labels for both the affine and deformable components of the registration. Results indicate that the best ANTs methods are competitive with existing brain extraction results (Jaccard=0.958) and cortical labeling approaches. Mutual information affine mapping combined with cross-correlation diffeomorphic mapping gave the best cortical labeling results (Jaccard=0.669±0.022). Furthermore, our two-fold cross-validation allows us to quantify the similarity of templates derived from different subgroups. Our open code, data and evaluation scripts set performance benchmark parameters for this state-of-the-art toolkit. This is the first study to use a consistent transformation framework to provide a reproducible evaluation of the isolated effect of the similarity metric on optimal template construction and brain labeling. Copyright © 2010 Elsevier Inc. All rights reserved.

            Author and article information

            1Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto ON, Canada
            2Krembil Research Institute, University Health Network, Toronto ON, Canada
            3Division of Neurosurgery, Toronto Western Hospital and University of Toronto, Toronto ON, Canada
            4Joint Department of Medical Imaging, University Health Network, Toronto ON, Canada
            Author notes

            Edited by: Jackson Cioni Bittencourt, University of São Paulo, Brazil

            Reviewed by: Hui-Yun Chang, National Tsing Hua University, Taiwan; Jingwen Niu, Temple University, USA

            *Correspondence: Mojgan Hodaie, smojgan.hodaie@
            Front Neuroanat
            Front Neuroanat
            Front. Neuroanat.
            Frontiers in Neuroanatomy
            Frontiers Media S.A.
            13 October 2016
            : 10
            5061742 10.3389/fnana.2016.00096
            Copyright © 2016 Chen, Zhong, Hayes, Behan, Walker, Hung and Hodaie.

            This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

            Figures: 7, Tables: 0, Equations: 1, References: 37, Pages: 11, Words: 0
            Funded by: Multiple Sclerosis Society of Canada 10.13039/501100000261
            Award ID: 2015, 1712
            Original Research


            Comment on this article