Tractography framework with magnetic resonance imaging for brain connectivity analysis
In white matter tractography from magnetic resonance imaging, a mathematical representation of diffusion (e.g., fiber orientation distributions) is first estimated from the diffusion MR data. Fiber tracing is performed via deterministic or probabilistic tractography where the tract maps and brain regions from multiple atlases and/or templates can be used for seeding and/or as spatial constraints. Field map correction and/or denoising may improve the diffusion weighted imaging data used in tractography.
1. A method for tractography with magnetic resonance imaging, the method comprising:
scanning a patient with a magnetic resonance imaging system for diffusion weighted data, the scanning providing data without diffusion sensitization and in phase-encoded and reverse phase encoded directions, the diffusion weighted data being in a subject space;
acquiring, with the magnetic resonance imaging system, structural magnetic resonance data;
correcting the diffusion weighted data with field maps estimated from the data acquired in the phase encoding and reverse phase encoding directions;
denoising the corrected diffusion weighted data;
registering a first atlas of tract maps to the subject space;
identifying regions of interest through which tracts of the tract maps pass from a second atlas;
generating a tractogram for the patient from the denoised, corrected diffusion weighted data, the tract maps, and the regions of interest; and
transmitting an image of the tractogram.
2. The method of claim 1 wherein scanning comprises performing diffusion magnetic resonance imaging.
3. The method of claim 1 wherein correcting comprises field map correcting.
4. The method of claim 1 wherein denoising comprises performing local principle component analysis.
5. The method of claim 1 wherein registering comprises registering the tract maps as probabilistic maps of fiber tracts.
6. The method of claim 1 wherein registering comprises determining first fractional anisotropy data from a fit of diffusion tensors to the denoised, corrected diffusion weighted data of the patient, nonlinearly registering the first fractional anisotropy data to second fractional anisotropy data of the first atlas, and warping the tract maps to the subject space based on the nonlinear registration.
7. The method of claim 1 wherein identifying comprises nonlinearly registering structural data representing the patient to structural data linked to the second atlas, warping the regions of interest of the second atlas based on the nonlinear registering, and identifying the regions of interest through which the tracts pass after the warping.
8. The method of claim 1 wherein generating comprises modeling diffusion with fiber orientation distributions from a constrained spherical deconvolution.
9. The method of claim 1 wherein generating comprises performing deterministic tractography guided by the regions of interest as seeded by the tract maps.
10. The method of claim 1 wherein transmitting comprises transmitting the image color coded as an axial tractogram, coronal tractogram, sagittal tractogram, or combinations thereof.
11. The method of claim 1 further comprising determining tract-specific regions as spatial constraints for the tracts from the first atlas, wherein generating the tractogram comprises generating the tractogram from the tract-specific regions.
12. The method of claim 1 further comprising:
masking skull from the diffusion weighted data;
registering the structural data for the patient with the data in the phase encoded direction; and
segmenting white matter and a white matter-gray matter interface from the structural data as registered;
wherein generating the tractogram comprises generating the tractogram from the white matter and the white matter-gray matter interface.
13. The method of claim 1 further comprising:
clustering tracts of the tractogram;
computing a biomarker map from the tractogram;
constructing a network or graph of the tracts of the tractogram; or
combinations thereof.