@article {1909,
	title = {Reproducibility and intercorrelation of graph theoretical measures in structural brain connectivity networks},
	journal = {Medical Image Analysis},
	volume = {52},
	year = {2019},
	pages = {56-67},
	doi = {https://doi.org/10.1016/j.media.2018.10.009},
	author = {Timo Roine and Ben Jeurissen and Daniele Perrone and Jan Aelterman and Wilfried Philips and Jan Sijbers and Alexander Leemans}
}
@article {1718,
	title = {High angular resolution diffusion-weighted imaging in mild traumatic brain injury},
	journal = {NeuroImage: Clinical},
	volume = {13},
	year = {2017},
	month = {11/2016},
	pages = {174 - 180},
	abstract = {We sought to investigate white matter abnormalities in mild traumatic brain injury (mTBI) using diffusion-weighted magnetic resonance imaging (DW-MRI). We applied a global approach based on tract-based spatial statistics skeleton as well as constrained spherical deconvolution tractography. DW-MRI was performed on 102 patients with mTBI within two months post-injury and 30 control subjects. A robust global approach considering only the voxels with a single-fiber configuration was used in addition to global analysis of the tract skeleton and probabilistic whole-brain tractography. In addition, we assessed whether the microstructural parameters correlated with age, time from injury, patient{\textquoteright}s outcome and white matter \{MRI\} hyperintensities. We found that whole-brain global approach restricted to single-fiber voxels showed significantly decreased fractional anisotropy (FA) (p = 0.002) and increased radial diffusivity (p = 0.011) in patients with mTBI compared with controls. The results restricted to single-fiber voxels were more significant and reproducible than those with the complete tract skeleton or the whole-brain tractography. \{FA\} correlated with patient outcomes, white matter hyperintensities and age. No correlation was observed between \{FA\} and time of scan post-injury. In conclusion, the global approach could be a promising imaging biomarker to detect white matter abnormalities following traumatic brain injury.},
	keywords = {Diffusion-weighted magnetic resonance imaging, Global approach, Magnetic Resonance Imaging, probabilistic tractography, Traumatic brain injury},
	issn = {2213-1582},
	doi = {http://dx.doi.org/10.1016/j.nicl.2016.11.016},
	url = {http://www.sciencedirect.com/science/article/pii/S2213158216302248},
	author = {Mohammadian, Mehrbod and Timo Roine and Jussi Hirvonen and Timo Kurki and Henna Ala-Sepp{\"a}l{\"a} and Janek Frantz{\'e}n and Ari Katila and Anna Kyll{\"o}nen and Henna-Riikka Maanp{\"a}{\"a} and Jussi Posti and Riikka Takala and Jussi Tallus and Olli Tenovuo}
}
@mastersthesis {1777,
	title = {Improved reliability of fiber orientation estimation and graph theoretical analysis of structural brain networks with diffusion MRI},
	volume = {Doctor of Science},
	year = {2017},
	school = {University of Antwerp},
	type = {PhD thesis},
	author = {Timo Roine}
}
@article {1651,
	title = {D-BRAIN: Anatomically Accurate Simulated Diffusion MRI Brain Data},
	journal = {PlosOne},
	volume = {11},
	number = {3},
	year = {2016},
	pages = {1-23},
	doi = {10.1371/journal.pone.0149778},
	author = {Daniele Perrone and Ben Jeurissen and Jan Aelterman and Timo Roine and Jan Sijbers and Aleksandra Pizurica and Alexander Leemans and Wilfried Philips}
}
@article {1634,
	title = {Abnormal wiring of the connectome in adults with high-functioning autism spectrum disorder},
	journal = {Molecular Autism},
	volume = {6},
	number = {1},
	year = {2015},
	pages = {65},
	abstract = {Recent brain imaging findings suggest that there are widely distributed abnormalities affecting the brain connectivity in individuals with autism spectrum disorder (ASD). Using graph theoretical analysis, it is possible to investigate both global and local properties of brain{\textquoteright}s wiring diagram, i.e., the connectome.
We acquired diffusion-weighted magnetic resonance imaging data from 14 adult males with high-functioning ASD and 19 age-, gender-, and IQ-matched controls. As with diffusion tensor imaging-based tractography, it is not possible to detect complex (e.g., crossing) fiber configurations, present in 60{\textendash}90 \% of white matter voxels; we performed constrained spherical deconvolution-based whole brain tractography. Unweighted and weighted structural brain networks were then reconstructed from these tractography data and analyzed with graph theoretical measures.
In subjects with ASD, global efficiency was significantly decreased both in the unweighted and the weighted networks, normalized characteristic path length was significantly increased in the unweighted networks, and strength was significantly decreased in the weighted networks. In the local analyses, betweenness centrality of the right caudate was significantly increased in the weighted networks, and the strength of the right superior temporal pole was significantly decreased in the unweighted networks in subjects with ASD.
Our findings provide new insights into understanding ASD by showing that the integration of structural brain networks is decreased and that there are abnormalities in the connectivity of the right caudate and right superior temporal pole in subjects with ASD.},
	keywords = {Autism spectrum disorder, Brain networks, Connectivity, Connectome, Diffusion Magnetic Resonance Imaging, Graph theoretical analysis, Tractography, White matter tract},
	issn = {2040-2392},
	doi = {10.1186/s13229-015-0058-4},
	url = {http://dx.doi.org/10.1186/s13229-015-0058-4},
	author = {Roine, Ulrika and Timo Roine and Salmi, Juha and Nieminen-von Wendt, Taina and Tani, Pekka and Lepp{\"a}m{\"a}ki, Sami and Rintahaka, Pertti and Caeyenberghs, Karen and Alexander Leemans and Sams, Mikko}
}
@article {1518,
	title = {Constrained spherical deconvolution-based tractography and tract-based spatial statistics show abnormal microstructural organization in Asperger syndrome},
	journal = {Molecular Autism},
	volume = {6},
	year = {2015},
	pages = {4},
	abstract = {Background: The aim of this study was to investigate potential differences in neural structure in individuals with Asperger syndrome (AS), high-functioning individuals with autism spectrum disorder (ASD). The main symptoms in AS are severe impairments in social interaction, and restricted or repetitive patterns of behavior, interests or activities. Methods: Diffusion weighted magnetic resonance imaging data was acquired for 14 adult males with AS and 19 age, gender and IQ-matched controls. Voxel-wise group differences in fractional anisotropy (FA) were studied with Tract-Based Spatial
Statistics (TBSS). Based on the results of TBSS, a tract-level comparison was performed with constrained spherical deconvolution (CSD)-based tractography, which is able to detect complex (e.g. crossing) fiber configurations. In addition, to investigate the relationship between the microstructural changes and the severity of symptoms, we looked for correlations between FA and Autism Spectrum Quotient (AQ), Empathy Quotient and Systemizing Quotient. Results: TBSS revealed widely distributed local increases in FA bilaterally in individuals with AS, most prominent in the temporal part of superior longitudinal fasciculus, corticospinal tract, splenium of corpus callosum, anterior thalamic radiation, inferior fronto-occipital fasciculus (IFO), posterior thalamic radiation, uncinate fasciculus and inferior longitudinal fasciculus (ILF). CSD-based tractography also showed increases in the FA in multiple tracts. However, only the difference in the left ILF was significant after a Bonferroni correction. These results were not explained by the complexity of microstructural organization, measured using the planar diffusion coefficient. In addition, we found a correlation between AQ and FA in the right IFO in the whole group. Conclusions: Our results suggest that there are local and tract-level abnormalities in WM microstructure in our homogenous and carefully characterized group of adults with AS, most prominent in the left ILF.},
	doi = {10.1186/2040-2392-6-4},
	url = {http://www.molecularautism.com/content/6/1/4},
	author = {Roine, Ulrika and Salmi, Juha and Timo Roine and Nieminen-von Wendt, Taina and Lepp{\"a}m{\"a}ki, Sami and Rintahaka, Pertti and Tani, Pekka and Alexander Leemans and Sams, Mikko}
}
@article {1519,
	title = {Informed constrained spherical deconvolution (iCSD)},
	journal = {Medical Image Analysis},
	volume = {24},
	year = {2015},
	pages = {269{\textendash}281},
	type = {Original research},
	chapter = {269},
	abstract = {Diffusion-weighted (DW) magnetic resonance imaging (MRI) is a noninvasive imaging method, which can be used to investigate neural tracts in the white matter (WM) of the brain. However, the voxel sizes used in DW-MRI are relatively large, making DW-MRI prone to significant partial volume effects (PVE). These PVEs can be caused both by complex (e.g. crossing) WM fiber configurations and non-WM tissue, such as gray matter (GM) and cerebrospinal fluid. High angular resolution diffusion imaging methods have been developed to correctly characterize complex WM fiber configurations, but significant non-WM PVEs are also present in a large proportion of WM voxels.
In constrained spherical deconvolution (CSD), the full fiber orientation distribution function (fODF) is deconvolved from clinically feasible DW data using a response function (RF) representing the signal of a single coherently oriented population of fibers. Non-WM PVEs cause a loss of precision in the detected fiber orientations and an emergence of false peaks in CSD, more prominently in voxels with GM PVEs. We propose a method, informed CSD (iCSD), to improve the estimation of fODFs under non-WM PVEs by modifying the RF to account for non-WM PVEs locally. In practice, the RF is modified based on tissue fractions estimated from high-resolution anatomical data.
Results from simulation and in-vivo bootstrapping experiments demonstrate a significant improvement in the precision of the identified fiber orientations and in the number of false peaks detected under GM PVEs. Probabilistic whole brain tractography shows fiber density is increased in the major WM tracts and decreased in subcortical GM regions. The iCSD method significantly improves the fiber orientation estimation at the WM-GM interface, which is especially important in connectomics, where the connectivity between GM regions is analyzed.},
	keywords = {Connectomics, constrained spherical deconvolution, Diffusion MRI, fiber orientation, gray matter, partial volume effect, Response function, Tractography},
	doi = {10.1016/j.media.2015.01.001},
	url = {http://www.sciencedirect.com/science/article/pii/S1361841515000080},
	author = {Timo Roine and Ben Jeurissen and Daniele Perrone and Jan Aelterman and Wilfried Philips and Alexander Leemans and Jan Sijbers}
}
@article {roine2015isotropic,
	title = {Isotropic non-white matter partial volume effects in constrained spherical deconvolution},
	journal = {Information-based methods for neuroimaging: analyzing structure, function and dynamics},
	year = {2015},
	pages = {112},
	publisher = {Frontiers Media SA},
	author = {Timo Roine and Ben Jeurissen and Daniele Perrone and Jan Aelterman and Alexander Leemans and Wilfried Philips and Jan Sijbers}
}
@conference {roine2014ismrm,
	title = {Improving fiber orientation estimation in constrained spherical deconvolution under non-white matter partial volume effects},
	year = {2014},
	month = {05/2014},
	pages = {4492},
	author = {Timo Roine and Ben Jeurissen and Wilfried Philips and Alexander Leemans and Jan Sijbers}
}
@article {roine2014frontiers,
	title = {Isotropic non-white matter partial volume effects in constrained spherical deconvolution},
	journal = {Frontiers in Neuroinformatics},
	volume = {8},
	number = {28},
	year = {2014},
	month = {03/2014},
	pages = {1-9},
	publisher = {Frontiers},
	type = {Original Research},
	abstract = {Diffusion-weighted (DW) magnetic resonance imaging (MRI) is a noninvasive imaging method, which can be used to investigate neural tracts in the white matter (WM) of the brain. Significant partial volume effects (PVE) are present in the DW signal due to relatively large voxel sizes. These PVEs can be caused by both non-WM tissue, such as gray matter (GM) and cerebrospinal fluid (CSF), and by multiple nonparallel WM fiber populations. High angular resolution diffusion imaging (HARDI) methods have been developed to correctly characterize complex WM fiber configurations, but to date, many of the HARDI methods do not account for non-WM PVEs. 

In this work, we investigated the isotropic PVEs caused by non-WM tissue in WM voxels on fiber orientations extracted with constrained spherical deconvolution (CSD). Experiments were performed on simulated and real DW-MRI data. In particular, simulations were performed to demonstrate the effects of varying the diffusion weightings, signal-to-noise ratios (SNR), fiber configurations, and tissue fractions. 

Our results show that the presence of non-WM tissue signal causes a decrease in the precision of the detected fiber orientations and an increase in the detection of false peaks in CSD. We estimated 35-50 \% of WM voxels to be affected by non-WM PVEs. For HARDI sequences, which typically have a relatively high degree of diffusion weighting, these adverse effects are most pronounced in voxels with GM PVEs. The non-WM PVEs become severe with 50 \% GM volume for maximum spherical harmonics orders of 8 and below, and already with 25 \% GM volume for higher orders. In addition, a low diffusion weighting or SNR increases the effects. 

The non-WM PVEs may cause problems in connectomics, where reliable fiber tracking at the WM-GM interface is especially important. We suggest acquiring data with high diffusion-weighting 2500-3000 s/mm2, reasonable SNR (~30) and using lower SH orders in GM contaminated regions to minimize the non-WM PVEs in CSD.
},
	keywords = {constrained spherical deconvolution, Diffusion MRI, fiber orientation, gray matter, partial volume effect},
	doi = {10.3389/fninf.2014.00028},
	url = {http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00028/abstract},
	author = {Timo Roine and Ben Jeurissen and Daniele Perrone and Jan Aelterman and Alexander Leemans and Wilfried Philips and Jan Sijbers}
}
@conference {1443,
	title = {Isotropic non-white matter partial volume effects in constrained spherical deconvolution},
	year = {2014},
	author = {Timo Roine and Ben Jeurissen and Wilfried Philips and Alexander Leemans and Jan Sijbers}
}
@conference {1433,
	title = {Analysis and modeling of isotropic partial volume effects in diffusion MRI},
	volume = {7},
	year = {2013},
	month = {2013},
	doi = {10.3389/conf.fninf.2013.10.00027},
	author = {Timo Roine and Ben Jeurissen and Alexander Leemans and Wilfried Philips and Jan Sijbers}
}
@article {1412,
	title = {Increased coherence of white matter fiber tract organization in adults with Asperger syndrome: A diffusion tensor imaging study},
	journal = {Autism Research},
	volume = {6},
	year = {2013},
	pages = {642-650},
	chapter = {642},
	doi = {10.1002/aur.1332},
	author = {Roine, Ulrika and Timo Roine and Salmi, Juha and Nieminen-von Wendt, Taina and Lepp{\"a}m{\"a}ki, Sami and Rintahaka, Pertti and Tani, Pekka and Alexander Leemans and Sams, Mikko}
}
@article {1413,
	title = {Reelin Associated With Restricted and Stereotyped Behavior Based on Principal Component Analysis on Autism Diagnostic Interview-Revised},
	journal = {Autism - Open Access},
	volume = {3},
	year = {2013},
	chapter = {107},
	url = {http://www.omicsgroup.org/journals/2165-7890/2165-7890-3-107.pdf},
	author = {Roine, Ulrika and Ripatti, Samuli and Rehnstr{\"o}m, Karola and Timo Roine and Kilpinen, Helena and Surakka, Ida and Wedenoja, Juho and Ylisaukko-oja, Tero and Kempas, Elli and Wessman, Jaana and Moilanen, Irma and Mattila, Marja-Leena and Kielinen, Marko and Jussila, Katja and Suomalainen, Saara and Pulkkinen, Esko and von Wendt, Lennart and Peltonen, Leena}
}
@conference {1415,
	title = {DTI-based Classification of Affection Status in Asperger Syndrome.},
	year = {2012},
	author = {Roine, Ulrika and Timo Roine and Salmi, Juha and Nieminen-von Wendt, Taina and Lepp{\"a}m{\"a}ki, Sami and Rintahaka, Pertti and Tani, Pekka and Sams, Mikko}
}
@inproceedings {1414,
	title = {Training Simulator for Flotation Process Operators},
	booktitle = {18th IFAC World Congress},
	year = {2011},
	url = {http://www.nt.ntnu.no/users/skoge/prost/proceedings/ifac11-proceedings/data/html/papers/2171.pdf},
	author = {Timo Roine and Kaartinen, Jani and Lamberg, Pertti}
}
@inproceedings {1417,
	title = {Development of a Machine Vision System to Monitor a Grinding Mill Prototype},
	booktitle = {12th European Symposium on Comminution and Classification (ESCC 2009)},
	year = {2009},
	author = {Timo Roine and Pietil{\"a}, Janne and Kaartinen, Jani and Blanz, Peter and Rantala, Pertti}
}
@inproceedings {1416,
	title = {Machine Vision of Flotation Froths with a Rapid-Prototyping Platform},
	booktitle = {IFAC Workshop on Automation in Mining, Mineral and Metal Industry (IFACMMM2009)},
	year = {2009},
	author = {Kaartinen, Jani and H{\"a}t{\"o}nen, Jari and Timo Roine}
}
