Super-Resolution Track Density Imaging of 1.4 mm isotropic 7T Whole-Brain Diffusion Magnetic Resonance Images
Ralf L├╝tzkendorf1, Robin M. Heidemann2, Thorsten Feiweier2, Michael Luchtmann3, Sebastian Baecke1, Joern Kaufmann4, Joerg Stadler5, Eike Budinger5, and Johannes Bernarding1

1Biometry and Medical Informatics, University of Magdeburg, Magdeburg, Germany, 2Siemens Healthcare GmbH, Erlangen, Germany, 3Department of Neurosurgery, University of Magdeburg, Magdeburg, Germany, 4Department of Neurology, University of Magdeburg, Magdeburg, Germany, 5Leibniz Institute for Neurobiology, Magdeburg, Germany


Track-density imaging (TDI) is a method to generate super-resolution images from fiber-tracking data (1). Here, we applied this technique to 1.4 mm isotropic 7T whole brain diffusion MR imaging data (dMRI). Besides the well-known large and medium-sized fiber tracts the high resolution of the data allowed visualizing the complex interwoven courses of fiber tracts in the cerebellar-pontine angle as well as showing parts of the trigeminus nerve. Combining TDI with high-resolved diffusion data has a great potential for analyzing the anatomy in vivo of brain structures across different scales as well as the neuronal connectome throughout the whole brain.


Using super-resolution track-density imaging (1) derived from isotropic high-resolution (1.4 mm) 7T diffusion data to analyze the connectome architecture through-out the whole human brain in vivo, ranging from large- to small-scale brain anatomic structures including midbrain and cerebellum.


Data were measured on a research 7 Tesla whole-body MR scanner (Siemens Healthcare GmbH, Germany), equipped with a 70 mT/m gradient coil (slew rate of 200 T/m/s). A 32-channel phased-array head coil (Nova Medical, USA) was used for head imaging. The protocol consisted of a high-resolution anatomic scan (MPRAGE, 0.8 mm isotropic resolution, covering the whole head including the cerebellum), diffusion-weighted MR images (dMRI) using a prototype single-shot-EPI sequence employing a modified Stejskal Tanner diffusion encoding gradient scheme (3,4). Additionally, a Gradient Echo sequence was acquired serving for B0 field mapping (5). Wwe optimized the diffusion gradients by employing a web application for multiple-shell protocol design provided by Caruyer (, consisting of 128 diffusion gradients per shell and different gradients in each shell. The dMRI protocol compromised 137 volumes with 1.4 mm isotropic resolution. We acquired 128 diffusion-weighted data sets (b=3000 s/mm2) with different combinations of gradient directions (6), and nine non-diffusion-weighted data sets (b=0 s/mm2, b0 images) interspersed with every 17th diffusion-weighted data set. EPI acquisition was accelerated using GRAPPA factor 3, 36 reference lines, 6/8 partial Fourier mode . Other imaging parameters were;bandwidth 1526 Hz/Pixel, echo spacing of 0.76 ms, TE = 73 ms, base resolution 156*156, 98 slices, field of view 220 mm), dMRI measurements coverd the whole brain including the cerebellum. Duration of the measurement was 50 minutes.Track-density images were generated according to MRTrix 3.0 ( The TD image was calculated from 10, 25 and 50 million tracts whole brain fibertracking and 1mm, 0.25mm and 0.15mm resolution.

Results and Discussion:

The results showed that due to the increased signal-to-noise ratio at 7T the quality of the high-resolved diffusion data was sufficient to acquire diffusion data without averaging (i.e. in one single acquisition). The high diffusion-weighting of b=3000 s/mm2 enabled a good delineation of crossing and bending fibers. The visual inspection and comparison of TDI data with different resolutions led to the conclusion that 10 million fibers, which is equivalent to a super-resolution of 0.2 mm, gave the best results. The fine anatomic details can be seen on exemplary slices (fig. 1, fig. 2; see figure captions for details). Most interestingly, the trigeminus nerve which is the largest brain nerve with a diameter of about 2.6 mm is clearly seen. The potential of 7T diffusion imaging to depict even small brain structures and details of the brain stem is also demonstrated by recent publications (6). The combination of ultra-high-field dMRI with super-resolution techniques is reported in (7,8,9). However, when planning to apply this technique in clinical diagnosis or even pre-surgical planning (e.h. for deep brain stimulation) a compromise has to be found between resolution and time for data acquisition. For whole-brain data we found that the resolution of 1.4 mm isotropic was the optimum (when applying high diffusion-weighting of b=3000 s/mm2) as data could be acquired in a single measurement without averaging. If very small structures such as thalamic nuclei have to be analyzed diffusion imaging techniques using restricted field-of-views (10,11) or techniques such as ZOOPPA (12) may allow increasing the resolution to sub-mm while acquisition time may still remain acceptable for patients. It is to be expected that sub-mm dMRI will allow increasing the super-resolution even further.


No acknowledgement found.


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Fig. 1: TDI with 25 million fibers derived from whole head diffusion tractograms based on 1.4 mm isotropic 7T diffusion data (left image: sagittal view; middle image: axial view; right image: coronal view). The high resolution depicts in great detail not only the larger fiber tracts but also the complex three-dimensionally interwoven connections between cortex, basal ganglia, pons and cerebellum as well as the anterior commissural fibers (arrow).

Fig. 2: Two adjacent axial TDI slices exhibiting the cerebellum, pons, transverse pontine fibers (red fiber bundles crossing horizontally at the ventral part of the pons and through the pons) and the large middle cerebellar peduncles (green) extending from the pons into the cerebellum. The arrows depict the extrapontine fibers of the trigeminus nerve. Due to the oblique position of the volunteer the exit points of the trigeminus at the pons appear somewhat shifted along the head-feet direction.

Proc. Intl. Soc. Mag. Reson. Med. 24 (2016)