references.bib

@ARTICLE{Yeh2019NDC,
  title    = "Differential tractography as a track-based biomarker for neuronal
              injury",
  author   = "Yeh, Fang-Cheng and Zaydan, Islam M and Suski, Valerie R and
              Lacomis, David and Richardson, R Mark and Maroon, Joseph C and
              Barrios-Martinez, Jessica",
  abstract = "Diffusion MRI tractography has been used to map the axonal
              structure of the human brain, but its ability to detect neuronal
              injury is yet to be explored. Here we report differential
              tractography, a new type of tractography that utilizes repeat MRI
              scans and a novel tracking strategy to map the exact segment of
              fiber pathways with a neuronal injury. We examined differential
              tractography on multiple sclerosis, Huntington's disease,
              amyotrophic lateral sclerosis, and epileptic patients. The
              results showed that the affected pathways shown by differential
              tractography matched well with the unique clinical symptoms of
              the patients, and the false discovery rate of the findings could
              be estimated using a sham setting to provide a reliability
              measurement. This novel approach enables a quantitative and
              objective method to monitor neuronal injury in individuals,
              allowing for diagnostic and prognostic evaluation of brain
              diseases.",
  journal  = "Neuroimage",
  volume   =  202,
  pages    = "116131",
  month    =  nov,
  year     =  2019,
  keywords = "Amyotrophic lateral sclerosis; Differential tractography;
              Diffusion MRI; Epilepsy; Fiber tracking; Huntington's disease;
              Imaging biomarker; Multiple sclerosis; Neuronal injury",
  language = "en"
}



@ARTICLE{Muncy2022GAMs,
  title    = "General additive models address statistical issues in diffusion
              {MRI}: An example with clinically anxious adolescents",
  author   = "Muncy, Nathan M and Kimbler, Adam and Hedges-Muncy, Ariana M and
              McMakin, Dana L and Mattfeld, Aaron T",
  abstract = "Statistical models employed to test for group differences in
              quantized diffusion-weighted MRI white matter tracts often fail
              to account for the large number of data points per tract in
              addition to the distribution, type, and interdependence of the
              data. To address these issues, we propose the use of Generalized
              Additive Models (GAMs) and supply code and examples to aid in
              their implementation. Specifically, using diffusion data from 73
              periadolescent clinically anxious and no-psychiatric-diagnosis
              control participants, we tested for group tract differences and
              show that a GAM allows for the identification of differences
              within a tract while accounting for the nature of the data as
              well as covariates and group factors. Further, we then used these
              tract differences to investigate their association with
              performance on a memory test. When comparing our high versus low
              anxiety groups, we observed a positive association between the
              left uncinate fasciculus and memory overgeneralization for
              negatively valenced stimuli. This same association was not
              evident in the right uncinate or anterior forceps. These findings
              illustrate that GAMs are well-suited for modeling diffusion data
              while accounting for various aspects of the data, and suggest
              that the adoption of GAMs will be a powerful investigatory tool
              for diffusion-weighted analyses.",
  journal  = "Neuroimage Clin",
  volume   =  33,
  pages    = "102937",
  month    =  jan,
  year     =  2022,
  keywords = "Adolescence; Anxiety; DWI; GAM; MRI; Uncinate",
  language = "en"
}
@ARTICLE{Kruper2021-az,
  title    = "Evaluating the Reliability of Human Brain White Matter
              Tractometry",
  author   = "Kruper, John and Yeatman, Jason D and Richie-Halford, Adam and
              Bloom, David and Grotheer, Mareike and Caffarra, Sendy and Kiar,
              Gregory and Karipidis, Iliana I and Roy, Ethan and Chandio,
              Bramsh Q and Garyfallidis, Eleftherios and Rokem, Ariel",
  journal  = "Apert Neuro",
  volume   =  1,
  number   =  1,
  month    =  nov,
  year     =  2021,
  keywords = "Brain Connectivity; Diffusion MRI; Reproducibility; Robustness;
              Tractography",

}
@ARTICLE{Andreasen1998-gg,
  title    = "``Cognitive dysmetria'' as an integrative theory of
              schizophrenia: a dysfunction in cortical-subcortical-cerebellar
              circuitry?",
  author   = "Andreasen, N C and Paradiso, S and O'Leary, D S",
  abstract = "Earlier efforts to localize the symptoms of schizophrenia in a
              single brain region have been replaced by models that postulate a
              disruption in parallel distributed or dynamic circuits. Based on
              empirical data derived from both magnetic resonance and positron
              emission tomography, we have developed a model that implicates
              connectivity among nodes located in prefrontal regions, the
              thalamic nuclei, and the cerebellum. A disruption in this
              circuitry produces ``cognitive dysmetria,'' difficulty in
              prioritizing, processing, coordinating, and responding to
              information. This ``poor mental coordination'' is a fundamental
              cognitive deficit in schizophrenia and can account for its broad
              diversity of symptoms.",
  journal  = "Schiz Bull",
  volume   =  24,
  number   =  2,
  pages    = "203--218",
  year     =  1998,
  language = "en"
}
@ARTICLE{Palesi2015-oi,
  title    = "Contralateral cerebello-thalamo-cortical pathways with prominent
              involvement of associative areas in humans in vivo",
  author   = "Palesi, Fulvia and Tournier, Jacques-Donald and Calamante,
              Fernando and Muhlert, Nils and Castellazzi, Gloria and Chard,
              Declan and D'Angelo, Egidio and Wheeler-Kingshott, Claudia A M",
  abstract = "In addition to motor functions, it has become clear that in
              humans the cerebellum plays a significant role in cognition too,
              through connections with associative areas in the cerebral
              cortex. Classical anatomy indicates that neo-cerebellar regions
              are connected with the contralateral cerebral cortex through the
              dentate nucleus, superior cerebellar peduncle, red nucleus and
              ventrolateral anterior nucleus of the thalamus. The anatomical
              existence of these connections has been demonstrated using virus
              retrograde transport techniques in monkeys and rats ex vivo. In
              this study, using advanced diffusion MRI tractography we show
              that it is possible to calculate streamlines to reconstruct the
              pathway connecting the cerebellar cortex with contralateral
              cerebral cortex in humans in vivo. Corresponding areas of the
              cerebellar and cerebral cortex encompassed similar proportion
              (about 80\%) of the tract, suggesting that the majority of
              streamlines passing through the superior cerebellar peduncle
              connect the cerebellar hemispheres through the ventrolateral
              thalamus with contralateral associative areas. This result
              demonstrates that this kind of tractography is a useful tool to
              map connections between the cerebellum and the cerebral cortex
              and moreover could be used to support specific theories about the
              abnormal communication along these pathways in cognitive
              dysfunctions in pathologies ranging from dyslexia to autism.",
  journal  = "Brain Struct. Funct.",
  volume   =  220,
  number   =  6,
  pages    = "3369--3384",
  month    =  nov,
  year     =  2015,
  keywords = "Cerebellum; Cerebral cortex; Diffusion MRI; MRI tractography",
  language = "en"
}
@ARTICLE{Jossinger2023-gj,
  title     = "The contributions of the cerebellar peduncles and the frontal
               aslant tract in mediating speech fluency",
  author    = "Jossinger, S and Yablonski, M and Amir, O and Ben-Shachar, M",
  abstract  = "Abstract Fluent speech production is a complex task that spans
               multiple processes, from conceptual framing and lexical access,
               through phonological encoding, to articulatory control. For the
               most part, imaging studies portraying the neural correlates of
               speech fluency tend to examine clinical populations sustaining
               speech impairments, and focus on either lexical access or
               articulatory control, but not both. Here, we evaluated the
               contribution of the cerebellar peduncles to speech fluency by
               measuring the different components of the process, in a sample
               of forty-five neurotypical adults. Participants underwent an
               unstructured interview to assess their natural speaking rate and
               articulation rate, and completed timed semantic and phonemic
               fluency tasks to assess their verbal fluency. Diffusion MRI with
               probabilistic tractography was used to segment the bilateral
               cerebellar peduncles (CPs) and frontal aslant tract (FAT),
               previously associated with speech production in clinical
               populations. Our results demonstrate distinct patterns of white
               matter associations with different fluency components.
               Specifically, verbal fluency is associated with the right
               superior CP, whereas speaking rate is associated with the right
               middle CP and bilateral FAT. No association is found with
               articulation rate in these pathways, in contrast to previous
               findings in persons who stutter. Our findings support the
               contribution of the cerebellum to aspects of speech production
               that go beyond articulatory control, such as lexical access,
               pragmatic or syntactic generation. Further, we demonstrate that
               distinct cerebellar pathways dissociate different components of
               speech fluency in neurotypical speakers.",
  journal   = "Neurobiol. Lang.",
  publisher = "MIT Press",
  pages     = "1--40",
  month     =  jan,
  year      =  2023,
  copyright = "https://creativecommons.org/licenses/by/4.0/",
  language  = "en"
}
@ARTICLE{Cao2018,
  title     = "Cerebello-thalamo-cortical hyperconnectivity as a state-
               independent functional neural signature for psychosis prediction
               and characterization",
  author    = "Cao, Hengyi and Chén, Oliver Y. and Chung, Yoonho and Forsyth,
               Jennifer K. and McEwen, Sarah C. and Gee, Dylan G. and Bearden,
               Carrie E. and Addington, Jean and Goodyear, Bradley and
               Cadenhead, Kristin S. and Mirzakhanian, Heline and Cornblatt,
               Barbara A. and Carrión, Ricardo E. and Mathalon, Daniel H. and
               McGlashan, Thomas H. and Perkins, Diana O. and Belger, Aysenil
               and Seidman, Larry J. and Thermenos, Heidi and Tsuang, Ming T.
               and van Erp, Theo G. M. and Walker, Elaine F. and Hamann,
               Stephan and Anticevic, Alan and Woods, Scott W. and Cannon,
               Tyrone D.",
  abstract  = "Understanding the fundamental alterations in brain functioning
               that lead to psychotic disorders remains a major challenge in
               clinical neuroscience. In particular, it is unknown whether any
               state-independent biomarkers can potentially predict the onset
               of psychosis and distinguish patients from healthy controls,
               regardless of paradigm. Here, using multi-paradigm fMRI data
               from the North American Prodrome Longitudinal Study consortium,
               we show that individuals at clinical high risk for psychosis
               display an intrinsic “trait-like” abnormality in brain
               architecture characterized as increased connectivity in the
               cerebello–thalamo–cortical circuitry, a pattern that is
               significantly more pronounced among converters compared with
               non-converters. This alteration is significantly correlated with
               disorganization symptoms and predictive of time to conversion to
               psychosis. Moreover, using an independent clinical sample, we
               demonstrate that this hyperconnectivity pattern is reliably
               detected and specifically present in patients with
               schizophrenia. These findings implicate
               cerebello–thalamo–cortical hyperconnectivity as a robust
               state-independent neural signature for psychosis prediction and
               characterization.",
  journal   = "Nature Communications",
  year      =  2018,
  month     =  sep,
  day       =  21,
  volume    =  9,
  number    =  1,
  pages     =  3836,
  issn      = "2041-1723",
}
@dataset{ds000030:1.0.0,
  author    = "Bilder, R and Poldrack, R and Cannon, T and London, E and
               Freimer, N and Congdon, E and Karlsgodt, K and Sabb, F",
  title     = "UCLA Consortium for Neuropsychiatric Phenomics LA5c Study",
  year      =  2020,
  publisher = "OpenNeuro",
}
@ARTICLE{Cieslak2021-vj,
  title    = "{QSIPrep}: an integrative platform for preprocessing and
              reconstructing diffusion {MRI} data",
  author   = "Cieslak, Matthew and Cook, Philip A and He, Xiaosong and Yeh,
              Fang-Cheng and Dhollander, Thijs and Adebimpe, Azeez and Aguirre,
              Geoffrey K and Bassett, Danielle S and Betzel, Richard F and
              Bourque, Josiane and Cabral, Laura M and Davatzikos, Christos and
              Detre, John A and Earl, Eric and Elliott, Mark A and Fadnavis,
              Shreyas and Fair, Damien A and Foran, Will and Fotiadis,
              Panagiotis and Garyfallidis, Eleftherios and Giesbrecht, Barry
              and Gur, Ruben C and Gur, Raquel E and Kelz, Max B and Keshavan,
              Anisha and Larsen, Bart S and Luna, Beatriz and Mackey, Allyson P
              and Milham, Michael P and Oathes, Desmond J and Perrone, Anders
              and Pines, Adam R and Roalf, David R and Richie-Halford, Adam and
              Rokem, Ariel and Sydnor, Valerie J and Tapera, Tinashe M and
              Tooley, Ursula A and Vettel, Jean M and Yeatman, Jason D and
              Grafton, Scott T and Satterthwaite, Theodore D",
  abstract = "Diffusion-weighted magnetic resonance imaging (dMRI) is the
              primary method for noninvasively studying the organization of
              white matter in the human brain. Here we introduce QSIPrep, an
              integrative software platform for the processing of diffusion
              images that is compatible with nearly all dMRI sampling schemes.
              Drawing on a diverse set of software suites to capitalize on
              their complementary strengths, QSIPrep facilitates the
              implementation of best practices for processing of diffusion
              images.",
  journal  = "Nat. Methods",
  volume   =  18,
  number   =  7,
  pages    = "775--778",
  month    =  jul,
  year     =  2021,
  language = "en"
}
@ARTICLE{Yeatman2012-ze,
  title    = "Tract profiles of white matter properties: automating fiber-tract
              quantification",
  author   = "Yeatman, Jason D and Dougherty, Robert F and Myall, Nathaniel J
              and Wandell, Brian A and Feldman, Heidi M",
  abstract = "Tractography based on diffusion weighted imaging (DWI) data is a
              method for identifying the major white matter fascicles (tracts)
              in the living human brain. The health of these tracts is an
              important factor underlying many cognitive and neurological
              disorders. In vivo, tissue properties may vary systematically
              along each tract for several reasons: different populations of
              axons enter and exit the tract, and disease can strike at local
              positions within the tract. Hence quantifying and understanding
              diffusion measures along each fiber tract (Tract Profile) may
              reveal new insights into white matter development, function, and
              disease that are not obvious from mean measures of that tract. We
              demonstrate several novel findings related to Tract Profiles in
              the brains of typically developing children and children at risk
              for white matter injury secondary to preterm birth. First,
              fractional anisotropy (FA) values vary substantially within a
              tract but the Tract FA Profile is consistent across subjects.
              Thus, Tract Profiles contain far more information than mean
              diffusion measures. Second, developmental changes in FA occur at
              specific positions within the Tract Profile, rather than along
              the entire tract. Third, Tract Profiles can be used to compare
              white matter properties of individual patients to standardized
              Tract Profiles of a healthy population to elucidate unique
              features of that patient's clinical condition. Fourth, Tract
              Profiles can be used to evaluate the association between white
              matter properties and behavioral outcomes. Specifically, in the
              preterm group reading ability is positively correlated with FA
              measured at specific locations on the left arcuate and left
              superior longitudinal fasciculus and the magnitude of the
              correlation varies significantly along the Tract Profiles. We
              introduce open source software for automated fiber-tract
              quantification (AFQ) that measures Tract Profiles of MRI
              parameters for 18 white matter tracts. With further validation,
              AFQ Tract Profiles have potential for informing clinical
              management and decision-making.",
  journal  = "PLoS One",
  volume   =  7,
  number   =  11,
  pages    = "e49790",
  month    =  nov,
  year     =  2012,
  language = "en"
}