Jakub Przemyslaw Piatkowski PhD

Jakub Piatkowski


Publications:
2012
  Segmenting white matter structure from diffusion MRI
Piatkowski, JP, Storkey, A & Bastin, M 2012, Segmenting white matter structure from diffusion MRI. in ICML Workshop on Statistics, Machine Learning and Neuroscience.
While diffusion MRI (dMRI) promises an insight into white matter integrity in vivo by measuring the degree of anisotropy in water molecule diffusion in the brain, the axonal pathways that connect different brain regions together can only partially be segmented using current methods. This is principally due to the lack of contrast in the spin-echo echo-planar MRI volumes collected in this modality. Here we present Tissue Dependent Diffusion model, a novel method for estimating the tissue composition of each voxel in the brain from dMRI data, thereby providing a foundation for computing the volume of different pathways in both health and disease.
General Information
Organisations: Edinburgh Imaging Facilities.
Authors: Piatkowski, Jakub Przemyslaw, Storkey, Amos & Bastin, Mark.
Publication Date: 2012
Publication Information
Category: Conference contribution
Original Language: English
  Probing the Brain's White Matter with Tissue Dependent Diffusion Model
Piatkowski, JP, Bastin, M & Storkey, A 2012, 'Probing the Brain's White Matter with Tissue Dependent Diffusion Model' SINAPSE Annual Scientific Meeting, Glasgow, United Kingdom, 30/05/12, .
While diffusion MRI (dMRI) promises an insight into white matter integrity in vivo, the axonal pathways that connect different brain regions together can only partially be segmented using current methods. Here we present a novel method for estimating the tissue composition of each voxel in the brain from dMRI data, thereby providing a foundation for computing the volume of different pathways in both health and disease. With our method, white matter (WM) is segmented by removing the ambiguity caused by the isotropic partial volumes (PV): both grey matter (GM) and cerebrospinal fluid (CSF). Apart from the volume fractions of all three tissue types we also obtain estimates of fibre orientations for tractography as well as diffusivity and anisotropy parameters which serve as proxy indices of pathway coherence. We assume Gaussian diffusion of water molecules for each tissue type. The resulting three-tensor model comprises one anisotropic (WM) compartment modelled by a cylindrical tensor and two isotropic compartments (CSF and GM).We model the measurement noise as Rician distributed. Markov chain Monte Carlo sampling techniques are used to estimate posterior distributions over the model's parameters. In particular, we employ Metropolis Hastings sampler with a custom burn-in and proposal adaptation to ensure good mixing and efficient exploration of the high-probability region. This way we obtain not only point estimates of quantities of interest, but also a measure of their uncertainty (posterior variance). We observe that the volume maps produced with our method show plausible and well delineated structures for all three tissue types. Estimated white matter fibre orientations also agree with known anatomy and align well with those obtained using the current methods. Importantly, we are able to disambiguate the volume and anisotropy information thus alleviating patrial volume effects and providing measures superior to the currently ubiquitous fractional anisotropy.
General Information
Organisations: Edinburgh Imaging Facilities.
Authors: Piatkowski, J P, Bastin, Mark & Storkey, Amos.
Publication Date: 2012
Publication Information
Category: Poster
Original Language: English
2010
  Discovering white matter structure beyond anisotropy maps with diffusion MRI
Piatkowski, JP, Bastin, M & Storkey, A 2010, 'Discovering white matter structure beyond anisotropy maps with diffusion MRI' ISMRM and ESMRMB Joint Annual Meeting, Stockholm, Sweden, 1/05/10 - 7/05/10, .
Diffusion MRI (dMRI) is the only method that allows in vivo segmentation of white matter (WM) fasciculi and assessment of their integrity, based on the water diffusion anisotropy caused by highly ordered bundles of axons. It can therefore be used to study wm decline: loss of integrity and tract thinning. The disambiguation of the volumetric and coherence information in the dmri data is not trivial. We show that it is possible to obtain reasonable estimates of: tract volume (on a sub-voxel level), local fibre orientation and diffusivity parameters linked to the coherence of axonal bundles, using a realistic model for mixed-tissue voxels and a plausible spatial similarity assumption.
General Information
Organisations: Edinburgh Imaging Facilities.
Authors: Piatkowski, Jakub Przemyslaw, Bastin, Mark & Storkey, Amos.
Publication Date: 2010
Publication Information
Category: Poster
Original Language: English
2009
  Estimating white matter tract volume in partial volume voxels with diffusion MRI
Piatkowski, JP, Bastin, M & Storkey, A 2009, 'Estimating white matter tract volume in partial volume voxels with diffusion MRI' ISMRM 17th Scientific Meeting and Exhibition, Honolulu, United States, 18/04/09 - 24/04/09, .
Diffusion MRI (dMRI) is the only method that allows in vivo segmentation of white matter (WM) fasciculi and assessment of their integrity, based on the water diffusion anisotropy caused by highly ordered bundles of axons. It can therefore be used to study wm decline: loss of integrity and tract thinning. Their disambiguation given the MRI data is not trivial. We show that it is possible to obtain reasonable estimates of both tract volume (on a sub-voxel level) and diffusivity parameters linked to the well being of axonal bundles using a plausible spatial coherence assumption.
General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Piatkowski, Jakub Przemyslaw, Bastin, Mark & Storkey, Amos.
Publication Date: 2009
Publication Information
Category: Poster
Original Language: English

Projects:
Realistic white matter models with high b-value, high angular resolution diffusion MRI (PhD)